Variant report

Variant	rs7939874
Chromosome Location	chr11:64661401-64661402
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	SP1	chr11:64660722-64661407	A549	lung:	n/a	chr11:64660958-64660967 chr11:64661060-64661069
2	POLR2A	chr11:64659817-64664484	K562	blood:	n/a	n/a
3	POLR2A	chr11:64659959-64662141	Hela-S3	cervix:	n/a	n/a
4	NR2F2	chr11:64660359-64662436	HepG2	liver:	n/a	n/a
5	POLR2A	chr11:64659833-64662055	K562	blood:	n/a	n/a
6	POLR2A	chr11:64660336-64662087	HepG2	liver:	n/a	n/a
7	CTCF	chr11:64660461-64662499	A549	lung:	n/a	chr11:64661476-64661486 chr11:64661906-64661916 chr11:64661898-64661919 chr11:64661904-64661920 chr11:64661909-64661918 chr11:64660964-64660973 chr11:64661903-64661921
8	POLR2A	chr11:64660273-64663920	K562	blood:	n/a	n/a
9	CHD1	chr11:64661392-64662215	IMR90	lung:	n/a	chr11:64661545-64661555
10	POLR2A	chr11:64655234-64662268	HepG2	liver:	n/a	n/a
11	HDAC2	chr11:64660600-64661438	HepG2	liver:	n/a	chr11:64661233-64661252
12	POLR2A	chr11:64660336-64662204	Hela-S3	cervix:	n/a	n/a
13	MYBL2	chr11:64661305-64662215	HepG2	liver:	n/a	n/a
14	TCF12	chr11:64659942-64662233	A549	lung:	n/a	chr11:64660845-64660855 chr11:64661175-64661185
15	MAX	chr11:64659774-64662203	A549	lung:	n/a	chr11:64661547-64661557
16	HEY1	chr11:64660286-64662151	HepG2	liver:	n/a	chr11:64661522-64661537
17	POLR2A	chr11:64660584-64661528	HepG2	liver:	n/a	n/a
18	POLR2A	chr11:64660471-64662158	GM12878	blood:	n/a	n/a
19	MTA3	chr11:64661149-64662261	GM12878	blood:	n/a	n/a
20	YY1	chr11:64660605-64661445	HepG2	liver:	n/a	chr11:64660848-64660859
21	POLR2A	chr11:64660447-64662045	A549	lung:	n/a	n/a
22	POLR2A	chr11:64661331-64662050	HepG2	liver:	n/a	n/a
23	POLR2A	chr11:64661239-64661538	K562	blood:	n/a	n/a
24	CTCF	chr11:64661280-64661430	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr11:64660386-64662157	GM12891	blood:	n/a	n/a
26	POLR2A	chr11:64661345-64661513	A549	lung:	n/a	n/a
27	ELF1	chr11:64661326-64662151	GM12878	blood:	n/a	n/a
28	MYBL2	chr11:64660346-64662255	HepG2	liver:	n/a	n/a
29	POLR2A	chr11:64660492-64662005	A549	lung:	n/a	n/a
30	POLR2A	chr11:64660338-64662053	HepG2	liver:	n/a	n/a
31	REST	chr11:64660541-64662119	A549	lung:	n/a	chr11:64661475-64661488
32	POLR2A	chr11:64660653-64662154	SK-N-MC	brain:	n/a	n/a
33	POLR2A	chr11:64661301-64661999	GM12878	blood:	n/a	n/a
34	POLR2A	chr11:64660762-64662466	K562	blood:	n/a	n/a
35	MAZ	chr11:64661374-64662154	IMR90	lung:	n/a	chr11:64661547-64661557
36	POLR2A	chr11:64660958-64661967	Hela-S3	cervix:	n/a	n/a
37	FOSL2	chr11:64660588-64662130	HepG2	liver:	n/a	n/a
38	POLR2A	chr11:64661172-64662021	GM12892	blood:	n/a	n/a
39	BCL3	chr11:64660723-64662145	A549	lung:	n/a	n/a
40	SMC3	chr11:64661222-64662212	SK-N-SH	brain:	n/a	chr11:64661911-64661919 chr11:64661905-64661919
41	POLR2A	chr11:64660132-64662075	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:64660891..64664747-chr11:64780644..64783500,5	K562	blood:
2	chr11:64660959..64663353-chr11:64681629..64685010,3	MCF-7	breast:
3	chr11:64614260..64615328-chr11:64661267..64662662,21	K562	blood:
4	chr11:64661385..64663055-chr11:64673353..64675725,2	MCF-7	breast:
5	chr11:64659914..64665589-chr11:64679566..64685622,11	K562	blood:
6	chr11:64660429..64663235-chr11:64780866..64783681,3	MCF-7	breast:
7	chr11:64660961..64662767-chr11:64683838..64685564,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203400	TF binding region
MIR192	TF binding region
MIR194-2	TF binding region
ENSG00000267804	TF binding region
ENSG00000068971	Chromatin interaction
ENSG00000213465	Chromatin interaction
ENSG00000110046	Chromatin interaction
ENSG00000273003	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs17146441	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2285346	0.84[CEU][hapmap];0.93[CHD][hapmap]
rs34944753	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs658006	0.87[ASN][1000 genomes]
rs7949887	0.81[CHB][hapmap];0.83[YRI][hapmap];0.82[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	nsv528506	chr11:64345448-64701030	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
2	nsv897695	chr11:64357072-64701030	Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
3	nsv897700	chr11:64447420-64701030	Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1071 gene(s)	inside rSNPs	diseases
4	nsv897704	chr11:64584987-64701030	Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
5	nsv897705	chr11:64591679-64701030	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
6	nsv897706	chr11:64591679-64721908	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
7	nsv897707	chr11:64600002-64701030	Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
8	nsv897708	chr11:64602757-64695271	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
9	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
10	nsv555208	chr11:64645119-64771179	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1029 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64655800-64663200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr11:64655800-64664600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr11:64655800-64672800	Weak transcription	Psoas Muscle	Psoas
4	chr11:64656000-64661600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr11:64656000-64661600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr11:64656000-64661600	Weak transcription	Esophagus	oesophagus
7	chr11:64656000-64661600	Weak transcription	Lung	lung
8	chr11:64656000-64662000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr11:64656000-64662000	Weak transcription	Brain Germinal Matrix	brain
10	chr11:64656000-64662000	Weak transcription	Brain Hippocampus Middle	brain
11	chr11:64656000-64662000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr11:64656000-64662000	Weak transcription	Ovary	ovary
13	chr11:64656000-64662000	Weak transcription	NHLF	lung
14	chr11:64656000-64662200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr11:64656000-64662200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr11:64656000-64662200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr11:64656000-64662200	Weak transcription	Brain Substantia Nigra	brain
18	chr11:64656000-64662200	Weak transcription	Thymus	Thymus
19	chr11:64656000-64662400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr11:64656000-64663000	Weak transcription	Primary T cells from cord blood	blood
21	chr11:64656000-64663200	Weak transcription	Brain Angular Gyrus	brain
22	chr11:64656000-64663600	Weak transcription	Brain Anterior Caudate	brain
23	chr11:64656000-64663800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr11:64656000-64664000	Weak transcription	Colon Smooth Muscle	Colon
25	chr11:64656000-64664200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr11:64656000-64664400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr11:64656000-64664600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr11:64656000-64665600	Weak transcription	HMEC	breast
29	chr11:64656000-64674200	Weak transcription	NH-A	brain
30	chr11:64656000-64677800	Weak transcription	HUVEC	blood vessel
31	chr11:64656000-64683200	Weak transcription	HSMM	muscle
32	chr11:64656000-64683400	Weak transcription	Right Atrium	heart
33	chr11:64656200-64661600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr11:64656200-64662000	Weak transcription	Dnd41	blood
35	chr11:64656400-64662200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr11:64656400-64663400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr11:64656600-64661600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr11:64656600-64661600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr11:64656600-64661600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr11:64656600-64662200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr11:64656600-64663600	Weak transcription	Osteobl	bone
42	chr11:64656600-64664200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr11:64656600-64664800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr11:64656600-64665200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr11:64656600-64668800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr11:64656600-64683400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr11:64656800-64661600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr11:64656800-64661800	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr11:64656800-64662000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
50	chr11:64656800-64662400	Weak transcription	H1 Cell Line	embryonic stem cell

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