Variant report

Variant	rs9809536
Chromosome Location	chr3:179068293-179068294
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:179039334..179043117-chr3:179061578..179071936,16	MCF-7	breast:
2	chr3:179040254..179044115-chr3:179063916..179068626,6	K562	blood:
3	chr3:179065090..179067243-chr3:179067855..179070398,3	K562	blood:
4	chr3:179068232..179070070-chr3:179073058..179075286,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171109	Chromatin interaction
ENSG00000121864	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10592	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13313931	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13327891	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6779649	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6780301	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6785443	1.00[EUR][1000 genomes]
rs6791769	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6795513	0.93[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808409	0.93[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7355960	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7356002	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7615773	1.00[EUR][1000 genomes]
rs9814990	1.00[EUR][1000 genomes]
rs9816934	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9820636	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9821850	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9869905	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9874433	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9877945	0.85[YRI][hapmap]
rs9883260	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv1002962	chr3:178943753-179224548	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv536815	chr3:178943753-179224548	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1003021	chr3:178944806-179246179	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv1006584	chr3:178944822-179241429	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv829806	chr3:178952363-179154373	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv471116	chr3:178968634-179252263	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv592650	chr3:178968634-179252263	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv1010513	chr3:178976107-179196274	Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv536816	chr3:178976107-179196274	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv1003514	chr3:178990037-179177029	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179066200-179071800	Weak transcription	Spleen	Spleen
2	chr3:179066200-179077400	Weak transcription	Small Intestine	intestine
3	chr3:179066200-179083800	Weak transcription	Aorta	Aorta
4	chr3:179066400-179069000	Weak transcription	Esophagus	oesophagus
5	chr3:179066400-179070000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:179066400-179070000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:179066400-179071400	Weak transcription	Lung	lung
8	chr3:179066400-179072600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:179066400-179073000	Weak transcription	Pancreas	Pancrea
10	chr3:179066400-179136600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:179066600-179069200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:179066600-179070200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:179066600-179071200	Weak transcription	A549	lung
14	chr3:179066600-179071400	Weak transcription	Right Ventricle	heart
15	chr3:179066800-179068400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr3:179066800-179068400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr3:179066800-179068400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr3:179066800-179068400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:179066800-179068400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:179066800-179068400	Weak transcription	HMEC	breast
21	chr3:179066800-179068400	Weak transcription	NHEK	skin
22	chr3:179066800-179068600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:179066800-179068600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:179066800-179068800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:179066800-179068800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:179066800-179069000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:179066800-179069000	Weak transcription	Brain Angular Gyrus	brain
28	chr3:179066800-179069000	Weak transcription	Brain Substantia Nigra	brain
29	chr3:179066800-179069000	Weak transcription	Colon Smooth Muscle	Colon
30	chr3:179066800-179069000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr3:179066800-179069000	Weak transcription	HUVEC	blood vessel
32	chr3:179066800-179069200	Genic enhancers	Primary B cells from peripheral blood	blood
33	chr3:179066800-179069200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr3:179066800-179069200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr3:179066800-179069200	Weak transcription	HSMMtube	muscle
36	chr3:179066800-179069400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:179066800-179069400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:179066800-179069400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:179066800-179069800	Weak transcription	Brain Anterior Caudate	brain
40	chr3:179066800-179069800	Weak transcription	Brain Hippocampus Middle	brain
41	chr3:179066800-179070200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr3:179066800-179071200	Weak transcription	Brain Germinal Matrix	brain
43	chr3:179066800-179071200	Weak transcription	NHLF	lung
44	chr3:179066800-179071400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr3:179066800-179071400	Weak transcription	Fetal Kidney	kidney
46	chr3:179066800-179071400	Weak transcription	Gastric	stomach
47	chr3:179066800-179071600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:179066800-179073400	Weak transcription	Psoas Muscle	Psoas
49	chr3:179066800-179073400	Weak transcription	Right Atrium	heart
50	chr3:179066800-179073800	Weak transcription	Colonic Mucosa	Colon

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