Variant report

Variant	rs3829062
Chromosome Location	chr9:71668197-71668198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71666774..71669833-chr9:71734752..71737934,3	MCF-7	breast:
2	chr9:71659255..71662171-chr9:71666375..71668806,2	K562	blood:
3	chr9:71661053..71663941-chr9:71667266..71670111,2	K562	blood:

Variant related genes	Relation type
ENSG00000119139	Chromatin interaction
ENSG00000165060	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10126006	0.91[CHB][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap]
rs10781379	0.82[CHB][hapmap]
rs10890	0.82[CHB][hapmap]
rs11145043	0.82[CHB][hapmap]
rs11145063	0.84[ASN][1000 genomes]
rs1411675	0.82[CHB][hapmap]
rs1411676	0.82[CHB][hapmap]
rs1815427	0.85[ASN][1000 genomes]
rs1888334	0.84[ASN][1000 genomes]
rs1984004	0.81[CHB][hapmap]
rs2309393	0.82[CHB][hapmap]
rs2309394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2481600	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2498427	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2498430	0.89[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.87[LWK][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2498431	0.89[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2498433	0.81[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2498434	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2871218	0.87[ASN][1000 genomes]
rs35104955	0.82[ASN][1000 genomes]
rs3793456	0.91[CHB][hapmap]
rs3793457	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3793459	0.91[ASN][1000 genomes]
rs3793460	0.90[ASN][1000 genomes]
rs3793461	0.82[CHB][hapmap]
rs3793465	0.81[CHB][hapmap]
rs3793466	0.82[CHB][hapmap]
rs3793467	0.82[CHB][hapmap]
rs3829064	0.92[CEU][hapmap];0.81[CHB][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4744807	0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.80[YRI][hapmap];0.87[ASN][1000 genomes]
rs4744808	0.82[CHB][hapmap]
rs4744811	0.82[ASN][1000 genomes]
rs4745553	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4745577	0.82[CHB][hapmap]
rs4745580	0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.80[YRI][hapmap];0.87[ASN][1000 genomes]
rs4745581	0.82[CHB][hapmap]
rs61290674	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6560547	0.80[ASN][1000 genomes]
rs6560550	0.80[ASN][1000 genomes]
rs6560551	0.80[ASN][1000 genomes]
rs7025834	0.86[ASN][1000 genomes]
rs7047274	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7849347	0.82[CHB][hapmap]
rs7855905	0.82[CHB][hapmap]
rs7861997	0.86[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs7865353	0.88[AMR][1000 genomes]
rs7870295	0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.87[ASN][1000 genomes]
rs7871596	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7875659	0.82[CHB][hapmap]
rs7875693	0.82[CHB][hapmap]
rs9314854	0.82[CHB][hapmap]
rs9411170	0.88[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9411171	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs944348	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1053402	chr9:71399722-71819949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv540146	chr9:71399722-71819949	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv1043689	chr9:71399922-71800338	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv540147	chr9:71399922-71800338	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv1047540	chr9:71401918-71803639	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	nsv466393	chr9:71453443-71704827	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv614547	chr9:71453443-71704827	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv1035823	chr9:71465139-71901672	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
13	nsv466396	chr9:71471912-71935577	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
14	nsv614548	chr9:71471912-71935577	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
15	nsv1051798	chr9:71511805-71792032	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
16	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
17	nsv466397	chr9:71574757-71843023	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
18	nsv614550	chr9:71574757-71843023	Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
19	nsv1050692	chr9:71578494-71843023	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
20	nsv893416	chr9:71597840-71888601	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
21	nsv1040539	chr9:71600042-71844108	Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
22	nsv540149	chr9:71600042-71844108	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
23	nsv949664	chr9:71607398-71842391	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
24	nsv466398	chr9:71612891-71671116	Flanking Active TSS Genic enhancers Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
25	nsv614551	chr9:71612891-71671116	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
26	nsv948708	chr9:71632265-71842391	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
27	nsv1037787	chr9:71635338-71807648	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
28	nsv540151	chr9:71635338-71807648	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
29	nsv893426	chr9:71659280-71719618	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
30	nsv1035268	chr9:71665139-71691673	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
31	nsv968705	chr9:71666410-71668674	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71651800-71680600	Weak transcription	HSMMtube	muscle
2	chr9:71652000-71672800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:71652000-71680600	Weak transcription	Brain Angular Gyrus	brain
4	chr9:71652000-71680800	Weak transcription	Primary B cells from cord blood	blood
5	chr9:71656600-71669800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr9:71658000-71670200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr9:71659600-71689800	Weak transcription	Colonic Mucosa	Colon
8	chr9:71659800-71683000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr9:71659800-71683000	Weak transcription	Psoas Muscle	Psoas
10	chr9:71659800-71685200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr9:71660000-71669000	Weak transcription	Stomach Mucosa	stomach
12	chr9:71660000-71669800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:71660000-71669800	Weak transcription	Hela-S3	cervix
14	chr9:71660000-71672600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr9:71660000-71679000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr9:71660000-71680800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr9:71660000-71682000	Weak transcription	NHLF	lung
18	chr9:71660000-71684400	Weak transcription	Small Intestine	intestine
19	chr9:71660000-71689400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr9:71661000-71675600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr9:71661200-71684800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr9:71662000-71671200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr9:71662000-71679800	Weak transcription	Fetal Kidney	kidney
24	chr9:71662400-71675400	Weak transcription	Fetal Heart	heart
25	chr9:71662600-71672600	Weak transcription	HSMM	muscle
26	chr9:71662800-71670000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr9:71662800-71686400	Weak transcription	Fetal Brain Female	brain
28	chr9:71663200-71670200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr9:71663600-71671000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr9:71664000-71674600	Weak transcription	HUVEC	blood vessel
31	chr9:71664000-71675400	Weak transcription	Brain Hippocampus Middle	brain
32	chr9:71664000-71675600	Weak transcription	Brain Substantia Nigra	brain
33	chr9:71664000-71675600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr9:71664000-71682000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr9:71664200-71669600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr9:71664200-71669800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr9:71664200-71671000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr9:71664200-71671200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr9:71664200-71672400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr9:71664200-71672600	Weak transcription	NHEK	skin
41	chr9:71664200-71675600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr9:71664200-71679400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr9:71664200-71680800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr9:71664200-71681400	Weak transcription	Right Ventricle	heart
45	chr9:71664200-71691200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr9:71664400-71668200	Weak transcription	Fetal Lung	lung
47	chr9:71664400-71669000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr9:71664400-71669200	Weak transcription	K562	blood
49	chr9:71664400-71669400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr9:71664400-71669600	Weak transcription	Dnd41	blood

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