Variant report

Variant	rs1662163
Chromosome Location	chr11:4115062-4115063
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:4114893-4115634	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:4115026-4116655	GM12892	blood:	n/a	n/a
3	POLR2A	chr11:4115051-4117511	U87	brain:	n/a	n/a
4	RCOR1	chr11:4115055-4117422	K562	blood:	n/a	n/a
5	POLR2A	chr11:4114949-4117449	U87	brain:	n/a	n/a
6	POLR2A	chr11:4114994-4116405	PANC-1	pancreas:	n/a	n/a
7	TEAD4	chr11:4115060-4116385	K562	blood:	n/a	n/a
8	REST	chr11:4115045-4117166	H1-neurons	neurons:	n/a	chr11:4115215-4115228
9	POLR2A	chr11:4115039-4116309	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr11:4114998-4116722	GM12878	blood:	n/a	n/a
11	POLR2A	chr11:4115003-4116673	GM18951	blood:	n/a	n/a
12	POLR2A	chr11:4115005-4117761	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr11:4115031-4117796	HepG2	liver:	n/a	n/a
14	POLR2A	chr11:4112420-4117868	K562	blood:	n/a	n/a
15	POLR2A	chr11:4114997-4116644	GM12891	blood:	n/a	n/a
16	POLR2A	chr11:4115040-4117205	K562	blood:	n/a	n/a
17	POLR2A	chr11:4115015-4116797	K562	blood:	n/a	n/a
18	POLR2A	chr11:4114936-4118198	Hela-S3	cervix:	n/a	n/a
19	HCFC1	chr11:4114838-4117374	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr11:4114955-4116463	HepG2	liver:	n/a	n/a
21	POLR2A	chr11:4114997-4116816	GM12892	blood:	n/a	n/a
22	POLR2A	chr11:4114998-4117877	GM12878	blood:	n/a	n/a
23	POLR2A	chr11:4113159-4117790	GM12891	blood:	n/a	n/a
24	POLR2A	chr11:4115042-4117215	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:4114277..4116935-chr11:4123036..4125551,3	K562	blood:
2	chr11:4108868..4111240-chr11:4112635..4115203,2	MCF-7	breast:
3	chr11:4109002..4112620-chr11:4113600..4116906,4	MCF-7	breast:
4	chr11:3859988..3862622-chr11:4113266..4115501,2	K562	blood:

No data

Variant related genes	Relation type
RRM1	TF binding region
ENSG00000167323	Chromatin interaction
ENSG00000177105	Chromatin interaction
ENSG00000167325	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10742229	0.87[CEU][hapmap]
rs10742249	1.00[JPT][hapmap]
rs10767853	0.82[CEU][hapmap]
rs10835678	0.92[EUR][1000 genomes]
rs11030814	0.87[CEU][hapmap]
rs1442725	0.87[CEU][hapmap]
rs1465952	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs1662177	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1735053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1735055	0.92[EUR][1000 genomes]
rs2289570	0.87[CEU][hapmap]
rs232045	0.92[EUR][1000 genomes]
rs2412341	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes]
rs2735690	0.92[EUR][1000 genomes]
rs2898950	0.87[CEU][hapmap]
rs2920141	0.87[CEU][hapmap]
rs2920142	0.87[CEU][hapmap]
rs2959071	0.87[CEU][hapmap]
rs2959072	0.87[CEU][hapmap]
rs4910881	0.87[CEU][hapmap]
rs6578445	0.92[EUR][1000 genomes]
rs7115615	0.92[EUR][1000 genomes]
rs7945918	0.86[CEU][hapmap]
rs894455	0.87[CEU][hapmap]
rs894457	0.85[EUR][1000 genomes]
rs9667777	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv896896	chr11:4010409-4185595	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2758253	chr11:4055945-4510188	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	esv2759797	chr11:4055945-4510188	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv428248	chr11:4055945-4510188	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv832053	chr11:4096527-4330263	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4086200-4115200	Weak transcription	NHDF-Ad	bronchial
2	chr11:4093800-4115200	Weak transcription	Fetal Kidney	kidney
3	chr11:4094000-4115200	Weak transcription	Brain Substantia Nigra	brain
4	chr11:4100200-4115200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr11:4100600-4115200	Weak transcription	NHLF	lung
6	chr11:4102400-4115200	Weak transcription	Fetal Brain Male	brain
7	chr11:4103000-4115200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:4103200-4115200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr11:4105800-4115200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr11:4106600-4115400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:4108200-4115200	Weak transcription	Brain Hippocampus Middle	brain
12	chr11:4108200-4115200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr11:4108200-4115400	Weak transcription	Small Intestine	intestine
14	chr11:4108400-4115200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr11:4108400-4115200	Weak transcription	Brain Anterior Caudate	brain
16	chr11:4108800-4115200	Weak transcription	Brain Angular Gyrus	brain
17	chr11:4109200-4115200	Weak transcription	HUVEC	blood vessel
18	chr11:4110000-4115200	Weak transcription	Placenta	Placenta
19	chr11:4112000-4115200	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr11:4112600-4115200	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr11:4113000-4115400	Weak transcription	Ovary	ovary
22	chr11:4113200-4115200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr11:4113200-4115200	Weak transcription	Fetal Brain Female	brain
24	chr11:4113200-4115200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr11:4113200-4115400	Weak transcription	Lung	lung
26	chr11:4113400-4115200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr11:4113400-4115200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr11:4113400-4115200	Weak transcription	Esophagus	oesophagus
29	chr11:4113400-4115400	Weak transcription	Gastric	stomach
30	chr11:4113400-4115400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr11:4113600-4115200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr11:4113600-4115200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr11:4113600-4115200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr11:4113600-4115200	Weak transcription	Colonic Mucosa	Colon
35	chr11:4113600-4115200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr11:4113600-4115200	Weak transcription	Thymus	Thymus
37	chr11:4113800-4115200	Enhancers	Primary T cells from cord blood	blood
38	chr11:4113800-4115200	Enhancers	Primary T cells fromperipheralblood	blood
39	chr11:4113800-4115200	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr11:4114000-4115200	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr11:4114000-4115200	Weak transcription	Primary hematopoietic stem cells	blood
42	chr11:4114000-4115200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr11:4114000-4115200	Weak transcription	Fetal Thymus	thymus
44	chr11:4114000-4115200	Weak transcription	K562	blood
45	chr11:4114600-4115200	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr11:4114800-4115200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr11:4114800-4115200	Enhancers	Liver	Liver
48	chr11:4114800-4115200	Enhancers	Fetal Muscle Leg	muscle
49	chr11:4114800-4115400	Enhancers	Pancreas	Pancrea
50	chr11:4114800-4115400	Enhancers	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links