Variant report

Variant	rs11171862
Chromosome Location	chr12:56871314-56871315
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56870750-56872115	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr12:56871002-56871416	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:56870847-56871321	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:56870924-56871948	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr12:56870830-56872070	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr12:56870904-56872002	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr12:56870616-56872078	ECC-1	luminal epithelium:	n/a	n/a
8	RUNX3	chr12:56871301-56871696	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:56870721-56872159	GM12892	blood:	n/a	n/a
10	POLR2A	chr12:56871018-56871534	PANC-1	pancreas:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56862204..56864692-chr12:56870931..56873632,2	MCF-7	breast:
2	chr12:56726518..56728953-chr12:56870711..56872482,2	MCF-7	breast:
3	chr12:56510179..56512052-chr12:56869735..56871547,2	MCF-7	breast:
4	chr12:56693028..56695003-chr12:56870939..56872704,2	MCF-7	breast:
5	chr12:56870822..56872349-chr12:56963864..56966406,2	MCF-7	breast:

No data

Variant related genes	Relation type
GLS2	TF binding region
ENSG00000062485	Chromatin interaction
ENSG00000135517	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000257303	Chromatin interaction
ENSG00000176422	Chromatin interaction
ENSG00000076067	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000135473	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10876895	0.96[ASN][1000 genomes]
rs11171863	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171865	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171870	0.82[ASN][1000 genomes]
rs12304519	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12313841	0.90[CEU][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs12316930	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12809550	0.83[EUR][1000 genomes]
rs12813881	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2638285	0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2638319	0.81[CEU][hapmap]
rs2638330	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2638334	0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638335	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2657909	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34287864	1.00[CEU][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs3809122	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58252713	0.90[ASN][1000 genomes]
rs6581096	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];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71459375	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71459376	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7314242	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[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	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv1052713	chr12:56848036-56917602	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11171862	RBMS2	Cis_1M	lymphoblastoid	RTeQTL
rs11171862	RBMS2	cis	cerebellum	SCAN
rs11171862	STAC3	cis	parietal	SCAN
rs11171862	SPRYD4	Cis_1M	lymphoblastoid	RTeQTL
rs11171862	FUT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56863200-56881000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:56863200-56881200	Weak transcription	Ovary	ovary
3	chr12:56863400-56873600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:56863400-56881000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr12:56863400-56881200	Weak transcription	Right Atrium	heart
6	chr12:56863400-56881400	Weak transcription	HSMMtube	muscle
7	chr12:56863600-56874200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr12:56863600-56880800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr12:56863800-56871400	Weak transcription	Brain Substantia Nigra	brain
10	chr12:56863800-56873400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr12:56863800-56879000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr12:56863800-56880800	Weak transcription	Brain Germinal Matrix	brain
13	chr12:56863800-56880800	Weak transcription	Gastric	stomach
14	chr12:56863800-56880800	Weak transcription	HMEC	breast
15	chr12:56863800-56881000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr12:56863800-56881200	Weak transcription	Colon Smooth Muscle	Colon
17	chr12:56863800-56881600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr12:56864000-56880600	Weak transcription	Thymus	Thymus
19	chr12:56864200-56874600	Weak transcription	K562	blood
20	chr12:56864200-56881200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr12:56864400-56880800	Weak transcription	Lung	lung
22	chr12:56864600-56873200	Weak transcription	Stomach Mucosa	stomach
23	chr12:56864800-56881000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr12:56865200-56873800	Strong transcription	Fetal Intestine Small	intestine
25	chr12:56865400-56873600	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr12:56865600-56872600	Strong transcription	Brain Angular Gyrus	brain
27	chr12:56865600-56873800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:56865600-56874600	Weak transcription	NHLF	lung
29	chr12:56865600-56875400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:56865600-56880800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr12:56865600-56881400	Weak transcription	Aorta	Aorta
32	chr12:56865800-56878000	Weak transcription	Fetal Stomach	stomach
33	chr12:56866000-56874200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:56866000-56880800	Weak transcription	Spleen	Spleen
35	chr12:56866000-56881000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr12:56866000-56881200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:56866200-56875200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:56866200-56881000	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr12:56866400-56874200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:56866400-56881000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr12:56866600-56874400	Weak transcription	NHEK	skin
42	chr12:56866600-56881200	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr12:56866800-56881200	Weak transcription	Primary B cells from cord blood	blood
44	chr12:56867200-56872800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr12:56867400-56873800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:56867400-56877200	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr12:56867400-56878400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr12:56867600-56871800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr12:56867600-56876600	Weak transcription	Dnd41	blood
50	chr12:56867600-56878400	Weak transcription	Fetal Brain Female	brain

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