Variant report

Variant	rs3827818
Chromosome Location	chr9:117669270-117669271
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	CTCF	chr9:117669228-117669535	K562	blood:	n/a	chr9:117669439-117669457 chr9:117669434-117669455 chr9:117669325-117669333
2	FOSL2	chr9:117669183-117671847	A549	lung:	n/a	chr9:117671336-117671347 chr9:117671340-117671349 chr9:117670747-117670756
3	RAD21	chr9:117669209-117669636	HepG2	liver:	n/a	chr9:117669437-117669456
4	CTCF	chr9:117669141-117669691	H1-hESC	embryonic stem cell:	n/a	chr9:117669439-117669457 chr9:117669434-117669455 chr9:117669325-117669333
5	RAD21	chr9:117669024-117669682	HCT-116	colon:	n/a	chr9:117669437-117669456
6	RAD21	chr9:117669252-117669512	GM12878	blood:	n/a	chr9:117669437-117669456
7	RAD21	chr9:117669131-117669610	ECC-1	luminal epithelium:	n/a	chr9:117669437-117669456
8	RAD21	chr9:117669079-117669592	SK-N-SH_RA	brain:	n/a	chr9:117669437-117669456
9	RAD21	chr9:117669201-117669641	A549	lung:	n/a	chr9:117669437-117669456
10	CTCF	chr9:117669265-117669628	A549	lung:	n/a	chr9:117669439-117669457 chr9:117669434-117669455 chr9:117669325-117669333
11	CTCF	chr9:117669239-117669626	ECC-1	luminal epithelium:	n/a	chr9:117669439-117669457 chr9:117669434-117669455 chr9:117669325-117669333
12	TEAD4	chr9:117669093-117669500	H1-hESC	embryonic stem cell:	n/a	n/a
13	SMC3	chr9:117669222-117669621	GM12878	blood:	n/a	chr9:117669441-117669455
14	YY1	chr9:117669216-117669619	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr9:117669180-117669638	HepG2	liver:	n/a	chr9:117669439-117669457 chr9:117669434-117669455 chr9:117669325-117669333
16	CTBP2	chr9:117669148-117669783	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr9:117669135-117669661	MCF-7	breast:	n/a	chr9:117669439-117669457 chr9:117669434-117669455 chr9:117669325-117669333
18	YY1	chr9:117669200-117669576	A549	lung:	n/a	n/a
19	FOXA2	chr9:117669196-117669613	A549	lung:	n/a	n/a
20	RAD21	chr9:117669075-117669781	HCT-116	colon:	n/a	chr9:117669437-117669456
21	SMC3	chr9:117669230-117669659	HepG2	liver:	n/a	chr9:117669441-117669455
22	CTCF	chr9:117669206-117669609	T-47D	breast:	n/a	chr9:117669439-117669457 chr9:117669434-117669455 chr9:117669325-117669333
23	RAD21	chr9:117669232-117669619	GM12878	blood:	n/a	chr9:117669437-117669456
24	RAD21	chr9:117669065-117669757	A549	lung:	n/a	chr9:117669437-117669456
25	SMC3	chr9:117669188-117669786	Hela-S3	cervix:	n/a	chr9:117669441-117669455
26	RAD21	chr9:117669128-117669731	MCF-7	breast:	n/a	chr9:117669437-117669456
27	CTCF	chr9:117669200-117669616	A549	lung:	n/a	chr9:117669439-117669457 chr9:117669434-117669455 chr9:117669325-117669333
28	MAZ	chr9:117669024-117669813	IMR90	lung:	n/a	n/a
29	GTF2F1	chr9:117669243-117669435	H1-hESC	embryonic stem cell:	n/a	n/a
30	RAD21	chr9:117668968-117670827	A549	lung:	n/a	chr9:117669437-117669456
31	RAD21	chr9:117669216-117669594	SK-N-SH_RA	brain:	n/a	chr9:117669437-117669456
32	CTCF	chr9:117669111-117669689	MCF-7	breast:	n/a	chr9:117669439-117669457 chr9:117669434-117669455 chr9:117669325-117669333
33	TCF12	chr9:117669001-117671706	A549	lung:	n/a	chr9:117670805-117670814 chr9:117671587-117671595
34	RAD21	chr9:117669018-117669862	SK-N-SH	brain:	n/a	chr9:117669437-117669456
35	SP1	chr9:117669092-117669645	A549	lung:	n/a	n/a
36	GATA2	chr9:117669259-117669718	HUVEC	blood vessel:	n/a	chr9:117669508-117669518 chr9:117669507-117669519 chr9:117669509-117669518 chr9:117669510-117669527 chr9:117669509-117669516
37	CTCF	chr9:117669180-117669330	GM12801	blood:	n/a	n/a
38	RAD21	chr9:117669093-117669725	H1-hESC	embryonic stem cell:	n/a	chr9:117669437-117669456
39	CTCF	chr9:117669122-117669707	A549	lung:	n/a	chr9:117669439-117669457 chr9:117669434-117669455 chr9:117669325-117669333
40	GATA3	chr9:117668450-117669740	MCF-7	breast:	n/a	chr9:117669508-117669518 chr9:117669507-117669519 chr9:117669509-117669518 chr9:117669510-117669527 chr9:117669509-117669516 chr9:117669095-117669105
41	CTCF	chr9:117669043-117669843	HCT-116	colon:	n/a	chr9:117669439-117669457 chr9:117669434-117669455 chr9:117669325-117669333
42	RAD21	chr9:117669081-117669670	H1-hESC	embryonic stem cell:	n/a	chr9:117669437-117669456
43	TBP	chr9:117669238-117669581	H1-hESC	embryonic stem cell:	n/a	n/a
44	FOXA2	chr9:117669093-117669603	A549	lung:	n/a	n/a
45	CTCF	chr9:117669153-117669699	HCT-116	colon:	n/a	chr9:117669439-117669457 chr9:117669434-117669455 chr9:117669325-117669333
46	CTCF	chr9:117669213-117669677	H1-hESC	embryonic stem cell:	n/a	chr9:117669439-117669457 chr9:117669434-117669455 chr9:117669325-117669333
47	RAD21	chr9:117669145-117669665	H1-hESC	embryonic stem cell:	n/a	chr9:117669437-117669456
48	CTCF	chr9:117669253-117669612	Gliobla	brain:	n/a	chr9:117669439-117669457 chr9:117669434-117669455 chr9:117669325-117669333
49	STAT3	chr9:117668887-117669345	MCF10A-Er-Src	breast:	n/a	n/a
50	SMC3	chr9:117668519-117670985	SK-N-SH	brain:	n/a	chr9:117669441-117669455

No.	Distal block	Cell Line	Cell type
1	chr9:117503657..117504194-chr9:117669070..117669921,2	MCF-7	breast:
2	chr9:117443784..117445753-chr9:117667939..117670651,2	MCF-7	breast:
3	chr9:117501292..117502939-chr9:117669201..117671782,2	MCF-7	breast:
4	chr1:121484470..121485223-chr9:117668926..117669480,2	MCF-7	breast:
5	chr9:117500707..117501777-chr9:117668813..117670087,8	MCF-7	breast:
6	chr9:117443571..117445056-chr9:117668906..117670084,6	MCF-7	breast:
7	chr9:117501090..117501824-chr9:117669215..117669812,2	K562	blood:
8	chr9:117500366..117501739-chr9:117668970..117671073,8	MCF-7	breast:
9	chr7:81293610..81294606-chr9:117669034..117669870,2	MCF-7	breast:
10	chr9:117442886..117445805-chr9:117668669..117671116,2	MCF-7	breast:
11	chr9:117497188..117498694-chr9:117669038..117671472,2	MCF-7	breast:

Variant related genes	Relation type
TNFSF8	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs16931962	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1885383	0.94[ASN][1000 genomes]
rs2181032	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3181194	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3181196	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3181357	0.84[ASN][1000 genomes]
rs3181360	0.91[ASN][1000 genomes]
rs3181362	0.86[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.99[ASN][1000 genomes]
rs3789878	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3789882	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4978612	0.91[ASN][1000 genomes]
rs55682128	1.00[AFR][1000 genomes]
rs55732631	1.00[AFR][1000 genomes]
rs55785761	1.00[AFR][1000 genomes]
rs56006049	1.00[AFR][1000 genomes]
rs56326427	1.00[AFR][1000 genomes]
rs6478118	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs7868670	0.92[ASN][1000 genomes]
rs7871914	0.92[ASN][1000 genomes]
rs973351	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831695	chr9:117567626-117726247	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv893767	chr9:117627569-117689838	Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117657800-117669600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr9:117661800-117669800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr9:117662200-117676200	Weak transcription	Gastric	stomach
4	chr9:117662800-117670600	Weak transcription	Esophagus	oesophagus
5	chr9:117663400-117672800	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr9:117663600-117672400	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr9:117664000-117670200	Weak transcription	HSMMtube	muscle
8	chr9:117664400-117670200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr9:117665400-117670200	Weak transcription	Osteobl	bone
10	chr9:117665400-117670400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:117665600-117669400	Weak transcription	HSMM	muscle
12	chr9:117665600-117671000	Weak transcription	NHLF	lung
13	chr9:117665800-117669400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr9:117665800-117669400	Weak transcription	Hela-S3	cervix
15	chr9:117665800-117669400	Weak transcription	NHEK	skin
16	chr9:117665800-117669600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr9:117665800-117670400	Genic enhancers	Primary T cells fromperipheralblood	blood
18	chr9:117665800-117670400	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr9:117665800-117672800	Weak transcription	Spleen	Spleen
20	chr9:117666000-117669400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr9:117666600-117670400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr9:117666600-117670400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr9:117667200-117669600	Enhancers	Fetal Intestine Small	intestine
24	chr9:117667400-117669400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr9:117667400-117670400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr9:117667400-117670600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr9:117667400-117673600	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr9:117667600-117669600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr9:117667600-117669800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr9:117667600-117670400	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr9:117667600-117673200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr9:117667800-117669400	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr9:117667800-117670200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr9:117667800-117683600	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr9:117668000-117670000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr9:117668200-117670200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr9:117668400-117670000	Enhancers	A549	lung
38	chr9:117668600-117669400	Enhancers	HUVEC	blood vessel
39	chr9:117668600-117671800	Enhancers	Placenta	Placenta
40	chr9:117668600-117672000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr9:117668800-117669400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr9:117668800-117669600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr9:117668800-117669600	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr9:117668800-117673400	Enhancers	Primary B cells from peripheral blood	blood
45	chr9:117668800-117673400	Enhancers	HMEC	breast
46	chr9:117669000-117671800	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr9:117669000-117672200	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr9:117669000-117674000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr9:117669200-117669400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr9:117669200-117669400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood

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