Variant report

Variant	rs182409
Chromosome Location	chr3:139238145-139238146
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:139238020-139238170	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:139220213..139222626-chr3:139237544..139240385,2	MCF-7	breast:

Variant related genes	Relation type
RBP1	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1007079	0.91[AMR][1000 genomes]
rs11914638	1.00[JPT][hapmap]
rs11919679	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11924964	1.00[JPT][hapmap]
rs12107249	1.00[JPT][hapmap]
rs1599926	1.00[JPT][hapmap]
rs1602627	0.91[AMR][1000 genomes]
rs188419	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs192688	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs211581	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs211584	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2233817	0.86[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2278577	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2307030	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs295475	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs295476	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295477	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3772874	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3772875	1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3821546	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs60082560	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60961550	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6439863	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6776315	0.82[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes]
rs72986799	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7373142	0.91[AMR][1000 genomes]
rs7373302	0.88[CEU][hapmap];0.82[CHB][hapmap];0.91[AMR][1000 genomes]
rs7622961	1.00[JPT][hapmap]
rs7648636	0.85[ASN][1000 genomes]
rs7649535	1.00[JPT][hapmap]
rs7651618	1.00[JPT][hapmap]
rs9819224	0.91[AMR][1000 genomes]
rs9858740	0.91[AMR][1000 genomes]
rs9859683	0.91[AMR][1000 genomes]
rs9879736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9879748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1001460	chr3:139194633-139241616	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139208200-139249600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:139213400-139239000	Weak transcription	Brain Substantia Nigra	brain
3	chr3:139223000-139247000	Weak transcription	Left Ventricle	heart
4	chr3:139227200-139238600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr3:139228600-139245000	Weak transcription	Spleen	Spleen
6	chr3:139228800-139253200	Weak transcription	Gastric	stomach
7	chr3:139231000-139252800	Weak transcription	Right Ventricle	heart
8	chr3:139232400-139244400	Weak transcription	HSMMtube	muscle
9	chr3:139233600-139238400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:139233800-139241200	Weak transcription	Fetal Brain Male	brain
11	chr3:139234400-139252600	Weak transcription	Lung	lung
12	chr3:139234600-139238800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:139234800-139250600	Weak transcription	Brain Angular Gyrus	brain
14	chr3:139234800-139251000	Weak transcription	Fetal Kidney	kidney
15	chr3:139234800-139251200	Weak transcription	Fetal Heart	heart
16	chr3:139235000-139253600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:139235200-139251400	Weak transcription	Liver	Liver
18	chr3:139235600-139238800	Weak transcription	Adipose Nuclei	Adipose
19	chr3:139235600-139239000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:139236000-139239000	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:139236000-139239200	Genic enhancers	Fetal Stomach	stomach
22	chr3:139236000-139239400	Genic enhancers	Fetal Muscle Trunk	muscle
23	chr3:139236000-139245200	Weak transcription	Brain Anterior Caudate	brain
24	chr3:139236400-139239200	Enhancers	Fetal Lung	lung
25	chr3:139236400-139250800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:139236600-139238600	Weak transcription	Pancreas	Pancrea
27	chr3:139236600-139245000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr3:139236600-139252000	Weak transcription	Right Atrium	heart
29	chr3:139236800-139238600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr3:139236800-139238600	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr3:139236800-139239400	Weak transcription	NH-A	brain
32	chr3:139237000-139239000	Genic enhancers	Fetal Muscle Leg	muscle
33	chr3:139237200-139249600	Weak transcription	Brain Germinal Matrix	brain
34	chr3:139237400-139238200	Weak transcription	Fetal Intestine Large	intestine
35	chr3:139237400-139238200	Weak transcription	Ovary	ovary
36	chr3:139237400-139238800	Weak transcription	Esophagus	oesophagus
37	chr3:139237600-139239600	Genic enhancers	Fetal Intestine Small	intestine
38	chr3:139237800-139239200	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr3:139237800-139241400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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