Variant report

Variant	rs11111771
Chromosome Location	chr12:104179271-104179272
allele	A/G
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	ARID3A	chr12:104179242-104179647	HepG2	liver:	n/a	n/a
2	FOXA2	chr12:104179114-104179345	HepG2	liver:	n/a	n/a
3	FOXA1	chr12:104179012-104179537	HepG2	liver:	n/a	n/a
4	CEBPB	chr12:104179122-104179394	HepG2	liver:	n/a	chr12:104179214-104179225
5	CEBPB	chr12:104179129-104179274	HepG2	liver:	n/a	chr12:104179214-104179225
6	FOXA1	chr12:104179100-104179414	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:104178636..104180567-chr12:104180995..104183516,2	K562	blood:
2	chr12:104178670..104180428-chr12:104186156..104188204,2	K562	blood:
3	chr12:104177175..104180567-chr12:104180842..104183516,3	K562	blood:

Variant related genes	Relation type
NT5DC3	TF binding region
ENSG00000111696	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10861094	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10861095	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10861096	0.91[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10861097	0.81[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10861099	0.85[TSI][hapmap]
rs10861104	0.90[ASW][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10861109	0.83[AFR][1000 genomes]
rs11111750	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11111752	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11111754	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11111755	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11111757	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11111758	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11111759	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11111762	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11111763	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11111765	0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11111767	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11111776	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11111778	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11111779	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11111791	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11111793	0.90[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs11111796	0.90[ASW][hapmap];0.83[CHB][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.85[AFR][1000 genomes]
rs11610714	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs12228207	0.82[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1370777	0.85[TSI][hapmap]
rs1565773	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs15918	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1866292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1976256	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2292682	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35371470	0.82[AFR][1000 genomes]
rs3751204	0.81[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3812805	0.81[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4964289	0.86[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs4964298	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4964780	0.83[CHB][hapmap];0.89[JPT][hapmap];0.85[AFR][1000 genomes]
rs4964820	0.85[TSI][hapmap]
rs4964823	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4964827	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4964830	0.81[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4981032	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4981036	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67825151	0.90[AFR][1000 genomes]
rs751448	0.81[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.81[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs869993	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9132	0.81[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs934843	0.87[TSI][hapmap]
rs934847	0.85[CEU][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs954920	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899480	chr12:104092996-104211440	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv899481	chr12:104092996-104213731	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv899482	chr12:104092996-104218956	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv899483	chr12:104117462-104218956	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv899487	chr12:104118587-104218956	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv899489	chr12:104144835-104218956	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv899490	chr12:104149022-104218956	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv899492	chr12:104151560-104183658	Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11111771	RP11-341G23.4	cis	Artery Tibial	GTEx
rs11111771	RP11-341G23.4	cis	Muscle Skeletal	GTEx
rs11111771	RP11-341G23.4	cis	Thyroid	GTEx
rs11111771	C12orf45	cis	cerebellum	SCAN
rs11111771	TU12B1-TY	cis	multi-tissue	Pritchard
rs11111771	RP11-341G23.4	cis	Esophagus Muscularis	GTEx
rs11111771	SKA3	trans	parietal	SCAN
rs11111771	NT5DC3	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104153200-104185200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:104154400-104186400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:104157400-104191200	Weak transcription	HUVEC	blood vessel
4	chr12:104160400-104185800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:104163600-104185000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr12:104163600-104204200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr12:104165800-104193400	Weak transcription	Fetal Lung	lung
8	chr12:104166400-104188400	Weak transcription	Fetal Thymus	thymus
9	chr12:104167200-104199800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:104168000-104185200	Weak transcription	Brain Germinal Matrix	brain
11	chr12:104168000-104190800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:104168600-104180800	Strong transcription	Stomach Smooth Muscle	stomach
13	chr12:104169000-104197800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:104169200-104180200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:104169600-104184800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr12:104170400-104180400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr12:104170600-104179400	Strong transcription	Primary B cells from peripheral blood	blood
18	chr12:104171200-104193600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr12:104171400-104188200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:104171600-104187400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr12:104171600-104194000	Weak transcription	Brain Substantia Nigra	brain
22	chr12:104171800-104187600	Weak transcription	Fetal Brain Female	brain
23	chr12:104171800-104216000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr12:104172400-104186400	Weak transcription	Brain Hippocampus Middle	brain
25	chr12:104172400-104191400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:104173000-104179400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:104173800-104208800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr12:104174000-104180400	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr12:104174000-104180400	Strong transcription	HMEC	breast
30	chr12:104174000-104194200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr12:104174200-104185200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr12:104174200-104186200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr12:104174400-104179800	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr12:104174800-104180400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:104175000-104179800	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr12:104175000-104180600	Strong transcription	HSMM	muscle
37	chr12:104175000-104187000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr12:104175200-104190000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr12:104175400-104179600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr12:104175800-104180400	Strong transcription	Colon Smooth Muscle	Colon
41	chr12:104175800-104180600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:104176200-104179400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:104176400-104179600	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr12:104176800-104179400	Strong transcription	Adipose Nuclei	Adipose
45	chr12:104176800-104180200	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr12:104176800-104180400	Strong transcription	Primary T cells from cord blood	blood
47	chr12:104176800-104181200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:104177000-104179400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr12:104177000-104179800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:104177000-104179800	Strong transcription	Aorta	Aorta

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