Variant report

Variant	rs113973
Chromosome Location	chr12:9244267-9244268
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	POLR2A	chr12:9242469-9248398	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:9242414-9246918	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:9244257-9246813	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:9242503-9246785	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
A2M	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10743598	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.94[LWK][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10771307	0.93[CHD][hapmap]
rs10771308	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10771309	0.93[CHD][hapmap]
rs10771357	0.89[JPT][hapmap]
rs10842789	0.86[CHD][hapmap]
rs10842839	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10842849	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11048789	0.93[CHD][hapmap]
rs11048839	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1805651	0.93[CHD][hapmap]
rs1805657	0.82[CHB][hapmap]
rs1805662	0.87[CHD][hapmap]
rs1805663	0.93[CHD][hapmap]
rs1805682	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2114851	0.89[JPT][hapmap]
rs2193006	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2216143	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs226369	0.89[JPT][hapmap]
rs226370	0.89[JPT][hapmap]
rs226372	0.89[JPT][hapmap]
rs226376	0.89[JPT][hapmap]
rs226379	0.93[CHD][hapmap]
rs226380	0.92[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs226381	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs226382	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs226384	0.87[CHD][hapmap]
rs226386	0.92[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs226387	0.92[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs226388	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs226389	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs226390	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs226391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs226392	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs226394	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs226400	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs226401	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs226403	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs226408	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226415	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3759276	0.89[JPT][hapmap]
rs3759277	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4882977	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4882981	0.84[JPT][hapmap]
rs6487584	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6487585	0.83[CHB][hapmap]
rs669	0.93[CHD][hapmap]
rs71453666	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7295733	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7297589	0.89[JPT][hapmap]
rs7955940	0.93[CHD][hapmap]
rs7964085	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7965790	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7976808	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832327	chr12:9081779-9246220	Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv898738	chr12:9205030-9274394	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
5	esv3504674	chr12:9243858-9318016	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3502154	chr12:9243906-9317851	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv3502155	chr12:9243906-9317851	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	esv3504685	chr12:9243948-9317959	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9218200-9266200	Weak transcription	Fetal Kidney	kidney
2	chr12:9219200-9266000	Weak transcription	Esophagus	oesophagus
3	chr12:9232200-9264600	Weak transcription	Brain Hippocampus Middle	brain
4	chr12:9232400-9244600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr12:9235000-9253600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:9235200-9265800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr12:9236600-9258800	Weak transcription	Fetal Heart	heart
8	chr12:9237200-9252200	Weak transcription	Psoas Muscle	Psoas
9	chr12:9237200-9261200	Strong transcription	Liver	Liver
10	chr12:9237200-9265200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:9237400-9264200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:9237600-9246000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:9237800-9258400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:9238600-9246800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:9238600-9265800	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr12:9238800-9246600	Strong transcription	Stomach Smooth Muscle	stomach
17	chr12:9239400-9262800	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr12:9239400-9264000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr12:9239600-9265000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:9240800-9267600	Weak transcription	Fetal Intestine Large	intestine
21	chr12:9241000-9246600	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr12:9241200-9246000	Strong transcription	Left Ventricle	heart
23	chr12:9241200-9247000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr12:9241200-9262800	Strong transcription	Adipose Nuclei	Adipose
25	chr12:9241600-9264000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:9242400-9246800	Strong transcription	Aorta	Aorta
27	chr12:9242400-9247000	Strong transcription	Ovary	ovary
28	chr12:9242600-9245400	Strong transcription	Rectal Smooth Muscle	rectum
29	chr12:9242600-9246200	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr12:9242800-9245200	Strong transcription	Gastric	stomach
31	chr12:9242800-9245600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr12:9242800-9246000	Strong transcription	Placenta	Placenta
33	chr12:9242800-9246800	Strong transcription	Fetal Stomach	stomach
34	chr12:9242800-9246800	Strong transcription	Spleen	Spleen
35	chr12:9243000-9246800	Strong transcription	Lung	lung
36	chr12:9243000-9251400	Weak transcription	Primary T cells from cord blood	blood
37	chr12:9243000-9274800	Weak transcription	Small Intestine	intestine
38	chr12:9243400-9244600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr12:9243400-9245400	Strong transcription	Colon Smooth Muscle	Colon
40	chr12:9243400-9245600	Weak transcription	Fetal Brain Male	brain
41	chr12:9243400-9265400	Weak transcription	Fetal Muscle Leg	muscle
42	chr12:9243600-9245200	Strong transcription	Colonic Mucosa	Colon
43	chr12:9243600-9247000	Strong transcription	Fetal Lung	lung
44	chr12:9243800-9244400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr12:9243800-9245600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr12:9243800-9252000	Strong transcription	HepG2	liver
47	chr12:9244000-9244800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:9244200-9244600	Strong transcription	Right Ventricle	heart
49	chr12:9244200-9265200	Weak transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links