Variant report

Variant	rs7977562
Chromosome Location	chr12:30836764-30836765
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:30835899..30838387-chr12:30843101..30844801,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11050995	0.84[ASN][1000 genomes]
rs11050996	0.92[ASN][1000 genomes]
rs11050997	0.92[ASN][1000 genomes]
rs11050998	0.92[ASN][1000 genomes]
rs11050999	0.92[ASN][1000 genomes]
rs11051000	0.92[ASN][1000 genomes]
rs11051001	0.92[ASN][1000 genomes]
rs11051004	0.92[ASN][1000 genomes]
rs11051011	1.00[ASN][1000 genomes]
rs11051014	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11051016	1.00[ASN][1000 genomes]
rs11051017	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051021	0.96[ASN][1000 genomes]
rs11051024	1.00[ASN][1000 genomes]
rs11051025	1.00[ASN][1000 genomes]
rs11051031	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11051032	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11051036	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11051039	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11051040	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs11051060	0.81[ASN][1000 genomes]
rs11051064	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11613738	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12229358	0.84[ASN][1000 genomes]
rs12229986	1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs12230006	0.81[ASN][1000 genomes]
rs12231670	1.00[ASN][1000 genomes]
rs16906596	0.92[ASN][1000 genomes]
rs16906601	0.92[ASN][1000 genomes]
rs16906606	0.92[ASN][1000 genomes]
rs16906713	0.94[ASN][1000 genomes]
rs16906758	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16916147	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3850959	0.84[ASN][1000 genomes]
rs3888018	0.82[JPT][hapmap]
rs3889761	0.92[ASN][1000 genomes]
rs57735299	0.92[ASN][1000 genomes]
rs60712960	0.92[ASN][1000 genomes]
rs7134692	1.00[CEU][hapmap]
rs7135640	1.00[CEU][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes]
rs7295175	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7970293	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3343291	chr12:30455597-30992837	Weak transcription Enhancers Strong transcription Active TSS Flanking 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	48 gene(s)	inside rSNPs	diseases
2	nsv832361	chr12:30794030-30997241	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv949148	chr12:30800040-31131712	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 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	chr12:30767000-30844200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:30780800-30847000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:30785000-30847800	Weak transcription	Gastric	stomach
4	chr12:30785200-30846400	Weak transcription	Spleen	Spleen
5	chr12:30785400-30847200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:30808000-30837800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:30808600-30839200	Strong transcription	Liver	Liver
8	chr12:30808800-30838000	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr12:30810000-30838200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:30810800-30843200	Strong transcription	Dnd41	blood
11	chr12:30810800-30843800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr12:30811000-30844200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:30812200-30837400	Strong transcription	Primary B cells from peripheral blood	blood
14	chr12:30812600-30844200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:30813000-30839400	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr12:30813200-30844200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr12:30813600-30844200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:30815400-30845800	Weak transcription	Fetal Brain Male	brain
19	chr12:30816200-30844000	Weak transcription	NHEK	skin
20	chr12:30816400-30844200	Weak transcription	NHLF	lung
21	chr12:30821600-30837600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr12:30821600-30844200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr12:30821800-30847200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr12:30821800-30847400	Weak transcription	Lung	lung
25	chr12:30822000-30846600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr12:30822600-30843800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr12:30822600-30845600	Weak transcription	Right Ventricle	heart
28	chr12:30822600-30846400	Weak transcription	Esophagus	oesophagus
29	chr12:30822600-30847400	Weak transcription	Aorta	Aorta
30	chr12:30822800-30839200	Weak transcription	Psoas Muscle	Psoas
31	chr12:30822800-30844200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:30825000-30837400	Strong transcription	Fetal Thymus	thymus
33	chr12:30825000-30839600	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr12:30826000-30845600	Weak transcription	Brain Germinal Matrix	brain
35	chr12:30826200-30837400	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr12:30827000-30847000	Weak transcription	Colonic Mucosa	Colon
37	chr12:30827800-30836800	Weak transcription	HepG2	liver
38	chr12:30827800-30844200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr12:30828200-30844200	Weak transcription	K562	blood
40	chr12:30829200-30838000	Weak transcription	Fetal Intestine Small	intestine
41	chr12:30829200-30844200	Weak transcription	Pancreas	Pancrea
42	chr12:30829600-30844200	Weak transcription	Small Intestine	intestine
43	chr12:30830200-30840600	Weak transcription	Brain Angular Gyrus	brain
44	chr12:30830400-30837200	Weak transcription	Fetal Kidney	kidney
45	chr12:30830400-30844000	Weak transcription	HMEC	breast
46	chr12:30830400-30844200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr12:30830400-30846600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr12:30830600-30843000	Weak transcription	HSMMtube	muscle
49	chr12:30830800-30839400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr12:30831000-30837200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links