Variant report

Variant	rs11111781
Chromosome Location	chr12:104187440-104187441
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104181732..104183493-chr12:104185105..104187662,2	K562	blood:
2	chr12:104186877..104189949-chr12:104233437..104236104,3	MCF-7	breast:
3	chr12:104186150..104188258-chr12:104233575..104235121,2	K562	blood:
4	chr12:104178670..104180428-chr12:104186156..104188204,2	K562	blood:
5	chr12:104183990..104193430-chr12:104193641..104204611,16	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257327	Chromatin interaction
ENSG00000111696	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10778285	0.99[ASN][1000 genomes]
rs10861093	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10861096	0.86[ASW][hapmap]
rs10861097	0.86[ASW][hapmap]
rs10861098	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10861099	0.86[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10861102	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10861103	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10861104	0.83[TSI][hapmap]
rs10861105	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs10861107	0.81[CHD][hapmap]
rs11111751	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11111761	0.90[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.99[ASN][1000 genomes]
rs11111764	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11111766	0.99[ASN][1000 genomes]
rs11111772	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111773	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111775	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111776	0.97[AFR][1000 genomes]
rs11111779	0.82[YRI][hapmap];0.91[AFR][1000 genomes]
rs11111782	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111783	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111786	0.96[AFR][1000 genomes]
rs11111787	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111788	0.98[AFR][1000 genomes]
rs11111789	0.95[AFR][1000 genomes]
rs11111792	0.89[AFR][1000 genomes]
rs11111795	0.82[GIH][hapmap]
rs12229276	0.82[GIH][hapmap]
rs12307138	0.81[CHD][hapmap]
rs12424737	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12425205	0.88[CHD][hapmap]
rs1370777	0.93[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1370778	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1370779	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1866293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866294	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[MEX][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]
rs1866295	1.00[ASW][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs1866296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs1968513	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2888792	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3751204	0.86[ASW][hapmap]
rs3751205	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3812804	0.81[CHD][hapmap]
rs4964794	1.00[ASW][hapmap];0.82[GIH][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs4964805	1.00[ASW][hapmap];0.82[GIH][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs4964806	1.00[ASW][hapmap];0.82[GIH][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs4964812	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs4964813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964814	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964819	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4964820	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4981035	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs5001722	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58421738	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs61602054	0.96[ASN][1000 genomes]
rs6539101	0.81[CHD][hapmap]
rs7134701	0.86[ASW][hapmap];0.82[GIH][hapmap]
rs7136682	0.93[ASN][1000 genomes]
rs7296900	1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.99[ASN][1000 genomes]
rs7312606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7312825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73192049	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73192053	0.85[AFR][1000 genomes]
rs7970553	0.81[CHD][hapmap]
rs7973081	0.99[ASN][1000 genomes]
rs9084	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9132	0.86[ASW][hapmap]
rs9142	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs934843	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs934845	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs934846	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs934847	0.93[ASW][hapmap];0.80[GIH][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs954921	0.86[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap]
rs9706225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11111781	TU12B1-TY	cis	multi-tissue	Pritchard
rs11111781	C12orf45	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104157400-104191200	Weak transcription	HUVEC	blood vessel
2	chr12:104163600-104204200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr12:104165800-104193400	Weak transcription	Fetal Lung	lung
4	chr12:104166400-104188400	Weak transcription	Fetal Thymus	thymus
5	chr12:104167200-104199800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:104168000-104190800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:104169000-104197800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:104171200-104193600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr12:104171400-104188200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:104171600-104194000	Weak transcription	Brain Substantia Nigra	brain
11	chr12:104171800-104187600	Weak transcription	Fetal Brain Female	brain
12	chr12:104171800-104216000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr12:104172400-104191400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr12:104173800-104208800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr12:104174000-104194200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:104175200-104190000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr12:104177800-104207600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:104178200-104187600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:104178400-104188400	Weak transcription	Brain Anterior Caudate	brain
20	chr12:104178600-104193400	Weak transcription	Left Ventricle	heart
21	chr12:104178800-104194000	Weak transcription	Brain Angular Gyrus	brain
22	chr12:104178800-104194200	Weak transcription	Esophagus	oesophagus
23	chr12:104179000-104188000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:104179000-104188400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr12:104179000-104188600	Weak transcription	Lung	lung
26	chr12:104179000-104190600	Weak transcription	Gastric	stomach
27	chr12:104179000-104193200	Weak transcription	Spleen	Spleen
28	chr12:104179000-104193600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr12:104179200-104188200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:104179400-104188400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr12:104179400-104191400	Weak transcription	Hela-S3	cervix
32	chr12:104179400-104193800	Weak transcription	Fetal Kidney	kidney
33	chr12:104179800-104192800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr12:104179800-104193800	Weak transcription	NHDF-Ad	bronchial
35	chr12:104180000-104188600	Weak transcription	HepG2	liver
36	chr12:104182400-104187600	Strong transcription	Stomach Smooth Muscle	stomach
37	chr12:104183600-104192800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:104183800-104193600	Weak transcription	Stomach Mucosa	stomach
39	chr12:104184200-104187800	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr12:104184800-104188600	Strong transcription	Fetal Stomach	stomach
41	chr12:104184800-104190400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr12:104184800-104192600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr12:104184800-104193400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:104185000-104187600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:104185000-104188200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr12:104185000-104189200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:104185000-104190800	Strong transcription	Fetal Muscle Trunk	muscle
48	chr12:104185000-104190800	Strong transcription	Fetal Muscle Leg	muscle
49	chr12:104185000-104191200	Strong transcription	Primary B cells from peripheral blood	blood
50	chr12:104185000-104191200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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