Variant report

Variant	rs3789882
Chromosome Location	chr9:117669699-117669700
allele	A/T
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	FOSL2	chr9:117669183-117671847	A549	lung:	n/a	chr9:117671336-117671347 chr9:117671340-117671349 chr9:117670747-117670756
2	CTBP2	chr9:117669148-117669783	H1-hESC	embryonic stem cell:	n/a	n/a
3	TFAP2C	chr9:117669344-117671438	Hela-S3	cervix:	n/a	chr9:117670616-117670631
4	RAD21	chr9:117669075-117669781	HCT-116	colon:	n/a	chr9:117669437-117669456
5	RAD21	chr9:117669065-117669757	A549	lung:	n/a	chr9:117669437-117669456
6	SMC3	chr9:117669188-117669786	Hela-S3	cervix:	n/a	chr9:117669441-117669455
7	RAD21	chr9:117669128-117669731	MCF-7	breast:	n/a	chr9:117669437-117669456
8	CTCF	chr9:117669680-117669830	HFF-Myc	foreskin:	n/a	n/a
9	MAZ	chr9:117669024-117669813	IMR90	lung:	n/a	n/a
10	RAD21	chr9:117668968-117670827	A549	lung:	n/a	chr9:117669437-117669456
11	MAZ	chr9:117669307-117669703	Hela-S3	cervix:	n/a	n/a
12	TCF12	chr9:117669001-117671706	A549	lung:	n/a	chr9:117670805-117670814 chr9:117671587-117671595
13	RAD21	chr9:117669018-117669862	SK-N-SH	brain:	n/a	chr9:117669437-117669456
14	GATA2	chr9:117669259-117669718	HUVEC	blood vessel:	n/a	chr9:117669508-117669518 chr9:117669507-117669519 chr9:117669509-117669518 chr9:117669510-117669527 chr9:117669509-117669516
15	RAD21	chr9:117669093-117669725	H1-hESC	embryonic stem cell:	n/a	chr9:117669437-117669456
16	CTCF	chr9:117669122-117669707	A549	lung:	n/a	chr9:117669439-117669457 chr9:117669434-117669455 chr9:117669325-117669333
17	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
18	CTCF	chr9:117669043-117669843	HCT-116	colon:	n/a	chr9:117669439-117669457 chr9:117669434-117669455 chr9:117669325-117669333
19	CTCF	chr9:117669153-117669699	HCT-116	colon:	n/a	chr9:117669439-117669457 chr9:117669434-117669455 chr9:117669325-117669333
20	CTCF	chr9:117669620-117669770	GM12865	blood:	n/a	n/a
21	SMC3	chr9:117668519-117670985	SK-N-SH	brain:	n/a	chr9:117669441-117669455
22	RAD21	chr9:117669192-117669829	Hela-S3	cervix:	n/a	chr9:117669437-117669456
23	CTCF	chr9:117668346-117670164	A549	lung:	n/a	chr9:117669439-117669457 chr9:117669434-117669455 chr9:117669325-117669333
24	CTCF	chr9:117669005-117670031	SK-N-SH	brain:	n/a	chr9:117669439-117669457 chr9:117669434-117669455 chr9:117669325-117669333
25	RAD21	chr9:117669076-117669725	MCF-7	breast:	n/a	chr9:117669437-117669456
26	CTCF	chr9:117669640-117669790	GM06990	blood:	n/a	n/a
27	RAD21	chr9:117669075-117669741	ECC-1	luminal epithelium:	n/a	chr9:117669437-117669456

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	chr9:117500707..117501777-chr9:117668813..117670087,8	MCF-7	breast:
5	chr9:117443571..117445056-chr9:117668906..117670084,6	MCF-7	breast:
6	chr9:117501090..117501824-chr9:117669215..117669812,2	K562	blood:
7	chr9:117500366..117501739-chr9:117668970..117671073,8	MCF-7	breast:
8	chr7:81293610..81294606-chr9:117669034..117669870,2	MCF-7	breast:
9	chr9:117442886..117445805-chr9:117668669..117671116,2	MCF-7	breast:
10	chr9:117497188..117498694-chr9:117669038..117671472,2	MCF-7	breast:

Variant related genes	Relation type
TNFSF8	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10817681	0.95[AFR][1000 genomes]
rs10982448	0.85[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes]
rs16931962	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs1885383	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2181032	0.91[ASN][1000 genomes]
rs3181192	1.00[TSI][hapmap]
rs3181194	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]
rs3181346	0.94[ASW][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs3181349	0.87[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs3181350	1.00[ASW][hapmap];0.87[CEU][hapmap];0.90[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs3181357	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3181359	0.88[AFR][1000 genomes]
rs3181360	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3181362	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3827818	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4978612	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4979462	0.82[MEX][hapmap]
rs61024439	0.88[AFR][1000 genomes]
rs6478118	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7854103	0.88[AFR][1000 genomes]
rs7868670	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7871914	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs973351	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:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117661800-117669800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr9:117662200-117676200	Weak transcription	Gastric	stomach
3	chr9:117662800-117670600	Weak transcription	Esophagus	oesophagus
4	chr9:117663400-117672800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr9:117663600-117672400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr9:117664000-117670200	Weak transcription	HSMMtube	muscle
7	chr9:117664400-117670200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr9:117665400-117670200	Weak transcription	Osteobl	bone
9	chr9:117665400-117670400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr9:117665600-117671000	Weak transcription	NHLF	lung
11	chr9:117665800-117670400	Genic enhancers	Primary T cells fromperipheralblood	blood
12	chr9:117665800-117670400	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr9:117665800-117672800	Weak transcription	Spleen	Spleen
14	chr9:117666600-117670400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr9:117666600-117670400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr9:117667400-117670400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr9:117667400-117670600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr9:117667400-117673600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr9:117667600-117669800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr9:117667600-117670400	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr9:117667600-117673200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr9:117667800-117670200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr9:117667800-117683600	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr9:117668000-117670000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr9:117668200-117670200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr9:117668400-117670000	Enhancers	A549	lung
27	chr9:117668600-117671800	Enhancers	Placenta	Placenta
28	chr9:117668600-117672000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr9:117668800-117673400	Enhancers	Primary B cells from peripheral blood	blood
30	chr9:117668800-117673400	Enhancers	HMEC	breast
31	chr9:117669000-117671800	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr9:117669000-117672200	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr9:117669000-117674000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr9:117669200-117669800	Enhancers	Fetal Stomach	stomach
35	chr9:117669200-117669800	Genic enhancers	Dnd41	blood
36	chr9:117669200-117669800	Enhancers	NHDF-Ad	bronchial
37	chr9:117669200-117670000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr9:117669200-117670000	Genic enhancers	Primary B cells from cord blood	blood
39	chr9:117669200-117670000	Enhancers	Duodenum Mucosa	Duodenum
40	chr9:117669200-117670200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr9:117669200-117670800	Enhancers	Primary T cells from cord blood	blood
42	chr9:117669200-117671200	Genic enhancers	Thymus	Thymus
43	chr9:117669200-117671400	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr9:117669200-117671600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr9:117669200-117671600	Enhancers	Placenta Amnion	Placenta Amnion
46	chr9:117669200-117671600	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr9:117669200-117672000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr9:117669200-117672000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr9:117669200-117672200	Enhancers	Fetal Lung	lung
50	chr9:117669200-117673200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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