Variant report

Variant	rs17292087
Chromosome Location	chr9:117669814-117669815
allele	C/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	FOSL2	chr9:117669183-117671847	A549	lung:	n/a	chr9:117671336-117671347 chr9:117671340-117671349 chr9:117670747-117670756
2	SP1	chr9:117669742-117671518	A549	lung:	n/a	chr9:117670738-117670759 chr9:117669925-117669939
3	TFAP2C	chr9:117669344-117671438	Hela-S3	cervix:	n/a	chr9:117670616-117670631
4	CTCF	chr9:117669680-117669830	HFF-Myc	foreskin:	n/a	n/a
5	RAD21	chr9:117668968-117670827	A549	lung:	n/a	chr9:117669437-117669456
6	CTCF	chr9:117669780-117669930	A549	lung:	n/a	n/a
7	TCF12	chr9:117669001-117671706	A549	lung:	n/a	chr9:117670805-117670814 chr9:117671587-117671595
8	CTCF	chr9:117669740-117669890	AG04450	lung:	n/a	n/a
9	RAD21	chr9:117669018-117669862	SK-N-SH	brain:	n/a	chr9:117669437-117669456
10	CTCF	chr9:117669043-117669843	HCT-116	colon:	n/a	chr9:117669439-117669457 chr9:117669434-117669455 chr9:117669325-117669333
11	EP300	chr9:117669748-117671608	A549	lung:	n/a	chr9:117670986-117671000
12	USF2	chr9:117669723-117669876	Hela-S3	cervix:	n/a	n/a
13	SMC3	chr9:117668519-117670985	SK-N-SH	brain:	n/a	chr9:117669441-117669455
14	RAD21	chr9:117669192-117669829	Hela-S3	cervix:	n/a	chr9:117669437-117669456
15	CTCF	chr9:117668346-117670164	A549	lung:	n/a	chr9:117669439-117669457 chr9:117669434-117669455 chr9:117669325-117669333
16	CTCF	chr9:117669005-117670031	SK-N-SH	brain:	n/a	chr9:117669439-117669457 chr9:117669434-117669455 chr9:117669325-117669333
17	CTCF	chr9:117669780-117669930	BJ	skin:	n/a	n/a

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	chr9:117500366..117501739-chr9:117668970..117671073,8	MCF-7	breast:
7	chr7:81293610..81294606-chr9:117669034..117669870,2	MCF-7	breast:
8	chr9:117442886..117445805-chr9:117668669..117671116,2	MCF-7	breast:
9	chr9:117497188..117498694-chr9:117669038..117671472,2	MCF-7	breast:

Variant related genes	Relation type
TNFSF8	TF binding region

Extended variants
information (count: 75 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1006025	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1006026	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1006027	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10081728	0.94[ASN][1000 genomes]
rs10817682	0.83[EUR][1000 genomes]
rs10817683	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10817684	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10817685	0.83[ASN][1000 genomes]
rs10982445	0.83[EUR][1000 genomes]
rs10982449	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10982450	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10982451	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10982453	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10982454	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10982455	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10982456	0.82[EUR][1000 genomes]
rs1126711	0.85[EUR][1000 genomes]
rs12337739	0.84[EUR][1000 genomes]
rs12338765	0.84[EUR][1000 genomes]
rs12347977	0.84[EUR][1000 genomes]
rs12352646	0.83[EUR][1000 genomes]
rs1322054	0.84[EUR][1000 genomes]
rs1322056	0.84[EUR][1000 genomes]
rs1322058	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1322059	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1322060	0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[ASN][1000 genomes]
rs1322067	0.85[EUR][1000 genomes]
rs1407309	0.82[EUR][1000 genomes]
rs1555456	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1555457	0.82[ASN][1000 genomes]
rs2075534	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2181033	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2181036	0.83[EUR][1000 genomes]
rs2208640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2295800	0.85[EUR][1000 genomes]
rs2418324	0.81[EUR][1000 genomes]
rs2418325	0.82[EUR][1000 genomes]
rs2974	0.84[EUR][1000 genomes]
rs3181195	1.00[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3181197	0.85[EUR][1000 genomes]
rs3181200	0.85[EUR][1000 genomes]
rs3181201	0.85[EUR][1000 genomes]
rs3181202	0.85[EUR][1000 genomes]
rs3181363	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3181364	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3181365	0.84[EUR][1000 genomes]
rs3181366	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3181367	0.84[EUR][1000 genomes]
rs3181368	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3181369	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3181370	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3181371	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3181372	0.84[EUR][1000 genomes]
rs3181374	0.85[EUR][1000 genomes]
rs3789879	0.84[EUR][1000 genomes]
rs4978611	0.84[EUR][1000 genomes]
rs4979470	0.82[EUR][1000 genomes]
rs4979471	0.83[EUR][1000 genomes]
rs4979472	0.82[EUR][1000 genomes]
rs4979473	0.94[ASN][1000 genomes]
rs6478117	0.84[EUR][1000 genomes]
rs7025577	0.84[EUR][1000 genomes]
rs7028578	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7030090	0.85[EUR][1000 genomes]
rs7032773	0.82[EUR][1000 genomes]
rs7036962	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7037640	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs726656	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs726657	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[ASN][1000 genomes]
rs7858603	0.85[EUR][1000 genomes]
rs7872878	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs927373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs927374	0.84[EUR][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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17292087	KIAA1958	cis	parietal	SCAN
rs17292087	ASTN2	cis	cerebellum	SCAN
rs17292087	SNORA70C	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117662200-117676200	Weak transcription	Gastric	stomach
2	chr9:117662800-117670600	Weak transcription	Esophagus	oesophagus
3	chr9:117663400-117672800	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr9:117663600-117672400	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr9:117664000-117670200	Weak transcription	HSMMtube	muscle
6	chr9:117664400-117670200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr9:117665400-117670200	Weak transcription	Osteobl	bone
8	chr9:117665400-117670400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:117665600-117671000	Weak transcription	NHLF	lung
10	chr9:117665800-117670400	Genic enhancers	Primary T cells fromperipheralblood	blood
11	chr9:117665800-117670400	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr9:117665800-117672800	Weak transcription	Spleen	Spleen
13	chr9:117666600-117670400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr9:117666600-117670400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr9:117667400-117670400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr9:117667400-117670600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr9:117667400-117673600	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr9:117667600-117670400	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr9:117667600-117673200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:117667800-117670200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr9:117667800-117683600	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr9:117668000-117670000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr9:117668200-117670200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr9:117668400-117670000	Enhancers	A549	lung
25	chr9:117668600-117671800	Enhancers	Placenta	Placenta
26	chr9:117668600-117672000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr9:117668800-117673400	Enhancers	Primary B cells from peripheral blood	blood
28	chr9:117668800-117673400	Enhancers	HMEC	breast
29	chr9:117669000-117671800	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr9:117669000-117672200	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr9:117669000-117674000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr9:117669200-117670000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr9:117669200-117670000	Genic enhancers	Primary B cells from cord blood	blood
34	chr9:117669200-117670000	Enhancers	Duodenum Mucosa	Duodenum
35	chr9:117669200-117670200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr9:117669200-117670800	Enhancers	Primary T cells from cord blood	blood
37	chr9:117669200-117671200	Genic enhancers	Thymus	Thymus
38	chr9:117669200-117671400	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr9:117669200-117671600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr9:117669200-117671600	Enhancers	Placenta Amnion	Placenta Amnion
41	chr9:117669200-117671600	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr9:117669200-117672000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:117669200-117672000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr9:117669200-117672200	Enhancers	Fetal Lung	lung
45	chr9:117669200-117673200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr9:117669200-117673800	Enhancers	Fetal Thymus	thymus
47	chr9:117669400-117670400	Weak transcription	HUVEC	blood vessel
48	chr9:117669400-117670800	Enhancers	Hela-S3	cervix
49	chr9:117669400-117670800	Enhancers	HSMM	muscle
50	chr9:117669400-117671000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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