Variant report

Variant	rs12337739
Chromosome Location	chr9:117670664-117670665
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	TEAD4	chr9:117670295-117670948	A549	lung:	n/a	n/a
2	PBX3	chr9:117670246-117670905	SK-N-SH	brain:	n/a	chr9:117670748-117670757
3	JUND	chr9:117670421-117670681	HepG2	liver:	n/a	n/a
4	FOSL2	chr9:117669183-117671847	A549	lung:	n/a	chr9:117671336-117671347 chr9:117671340-117671349 chr9:117670747-117670756
5	KAP1	chr9:117670367-117670931	HEK293	kidney:	n/a	n/a
6	NR3C1	chr9:117670297-117670822	A549	lung:	n/a	chr9:117670729-117670755
7	BCL3	chr9:117670204-117670998	A549	lung:	n/a	n/a
8	CREB1	chr9:117670488-117670863	A549	lung:	n/a	n/a
9	MYC	chr9:117670318-117671027	MCF10A-Er-Src	breast:	n/a	n/a
10	NR3C1	chr9:117670210-117670904	A549	lung:	n/a	chr9:117670729-117670755
11	SIN3AK20	chr9:117670275-117670845	A549	lung:	n/a	n/a
12	SIN3AK20	chr9:117670232-117670824	A549	lung:	n/a	n/a
13	TEAD4	chr9:117670223-117670872	A549	lung:	n/a	n/a
14	EP300	chr9:117670393-117670726	HepG2	liver:	n/a	n/a
15	FOSL2	chr9:117670322-117670852	SK-N-SH	brain:	n/a	chr9:117670747-117670756
16	GATA3	chr9:117670142-117670913	T-47D	breast:	n/a	chr9:117670692-117670699 chr9:117670685-117670706 chr9:117670687-117670703 chr9:117670609-117670617 chr9:117670839-117670847 chr9:117670692-117670699 chr9:117670692-117670699
17	RXRA	chr9:117670288-117671004	SK-N-SH	brain:	n/a	n/a
18	STAT3	chr9:117670504-117670946	MCF10A-Er-Src	breast:	n/a	chr9:117670902-117670916
19	CEBPB	chr9:117670136-117670979	A549	lung:	n/a	n/a
20	ZBTB33	chr9:117670238-117670865	A549	lung:	n/a	n/a
21	ZBTB33	chr9:117670345-117670906	SK-N-SH	brain:	n/a	n/a
22	CREB1	chr9:117670345-117670723	A549	lung:	n/a	n/a
23	SP1	chr9:117669742-117671518	A549	lung:	n/a	chr9:117670738-117670759 chr9:117669925-117669939
24	CBX3	chr9:117670347-117670878	HCT-116	colon:	n/a	n/a
25	FOXA1	chr9:117670247-117670864	HepG2	liver:	n/a	n/a
26	FOXA2	chr9:117670066-117670927	HepG2	liver:	n/a	n/a
27	GATA3	chr9:117670121-117670930	T-47D	breast:	n/a	chr9:117670692-117670699 chr9:117670685-117670706 chr9:117670687-117670703 chr9:117670609-117670617 chr9:117670839-117670847 chr9:117670692-117670699 chr9:117670692-117670699
28	TBP	chr9:117670312-117670944	Hela-S3	cervix:	n/a	n/a
29	GATA3	chr9:117670359-117670925	MCF-7	breast:	n/a	chr9:117670692-117670699 chr9:117670685-117670706 chr9:117670687-117670703 chr9:117670609-117670617 chr9:117670839-117670847 chr9:117670692-117670699 chr9:117670692-117670699
30	PRDM1	chr9:117670415-117670841	Hela-S3	cervix:	n/a	n/a
31	JUND	chr9:117670095-117670993	MCF-7	breast:	n/a	chr9:117670747-117670756
32	STAT3	chr9:117670265-117670910	Hela-S3	cervix:	n/a	n/a
33	EP300	chr9:117670205-117671110	SK-N-SH	brain:	n/a	chr9:117670986-117671000
34	SP1	chr9:117669957-117671066	A549	lung:	n/a	chr9:117670738-117670759
35	MAFF	chr9:117670416-117670738	HepG2	liver:	n/a	n/a
36	CEBPB	chr9:117670214-117670931	MCF-7	breast:	n/a	n/a
37	CEBPB	chr9:117670283-117670896	A549	lung:	n/a	n/a
38	FOXA1	chr9:117670196-117670856	HepG2	liver:	n/a	n/a
39	TFAP2C	chr9:117669344-117671438	Hela-S3	cervix:	n/a	chr9:117670616-117670631
40	TFAP2A	chr9:117670122-117671478	Hela-S3	cervix:	n/a	chr9:117670620-117670631 chr9:117670615-117670630 chr9:117670704-117670714 chr9:117670618-117670632 chr9:117670616-117670631 chr9:117670620-117670631 chr9:117670620-117670631 chr9:117670620-117670631
41	ESR1	chr9:117670288-117670864	T-47D	breast:	n/a	n/a
42	BRCA1	chr9:117670248-117670950	Hela-S3	cervix:	n/a	n/a
43	FOSL2	chr9:117670253-117670841	A549	lung:	n/a	chr9:117670747-117670756
44	MAZ	chr9:117670255-117670818	Hela-S3	cervix:	n/a	n/a
45	EP300	chr9:117670137-117670923	T-47D	breast:	n/a	n/a
46	CTCF	chr9:117670620-117670770	WERI-Rb-1	eye:	n/a	n/a
47	GATA3	chr9:117670142-117670996	A549	lung:	n/a	chr9:117670692-117670699 chr9:117670685-117670706 chr9:117670687-117670703 chr9:117670609-117670617 chr9:117670839-117670847 chr9:117670692-117670699 chr9:117670692-117670699
48	POLR2A	chr9:117670266-117670790	SK-N-SH	brain:	n/a	n/a
49	MAX	chr9:117670297-117670878	SK-N-SH	brain:	n/a	n/a
50	FOXA1	chr9:117670148-117670913	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:117501292..117502939-chr9:117669201..117671782,2	MCF-7	breast:
2	chr9:117500366..117501739-chr9:117668970..117671073,8	MCF-7	breast:
3	chr9:117442886..117445805-chr9:117668669..117671116,2	MCF-7	breast:
4	chr9:117497188..117498694-chr9:117669038..117671472,2	MCF-7	breast:

Variant related genes	Relation type
TNFSF8	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1006025	0.82[EUR][1000 genomes]
rs1006026	0.94[EUR][1000 genomes]
rs1006027	0.82[EUR][1000 genomes]
rs10081728	0.83[EUR][1000 genomes]
rs10817679	0.90[ASN][1000 genomes]
rs10817682	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10817683	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs10817685	0.80[EUR][1000 genomes]
rs10982445	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10982449	0.82[EUR][1000 genomes]
rs10982450	0.84[EUR][1000 genomes]
rs10982451	0.83[EUR][1000 genomes]
rs10982453	0.82[EUR][1000 genomes]
rs10982454	0.82[EUR][1000 genomes]
rs10982455	0.82[EUR][1000 genomes]
rs10982456	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1126711	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12338765	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12347977	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12352646	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1322054	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1322056	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1322058	0.83[EUR][1000 genomes]
rs1322060	0.85[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs1322067	0.97[EUR][1000 genomes]
rs1407309	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17292087	0.84[EUR][1000 genomes]
rs2075533	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2181036	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2208640	0.83[EUR][1000 genomes]
rs2295800	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2418324	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2418325	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2974	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3181195	0.84[EUR][1000 genomes]
rs3181197	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181200	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3181201	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3181202	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3181348	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3181363	0.82[EUR][1000 genomes]
rs3181364	0.83[EUR][1000 genomes]
rs3181365	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181366	0.83[EUR][1000 genomes]
rs3181367	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3181368	0.84[EUR][1000 genomes]
rs3181369	0.84[EUR][1000 genomes]
rs3181370	0.84[EUR][1000 genomes]
rs3181371	0.84[EUR][1000 genomes]
rs3181372	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3181374	0.82[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3789879	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4978611	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4979470	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4979471	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4979472	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4979473	0.84[EUR][1000 genomes]
rs6478117	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7025577	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7028578	0.84[EUR][1000 genomes]
rs7030090	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7032773	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7036962	0.82[EUR][1000 genomes]
rs7037640	0.84[EUR][1000 genomes]
rs726657	0.89[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs7858603	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7872878	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs911603	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs927373	0.82[EUR][1000 genomes]
rs927374	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs927375	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12337739	ASTN2	cis	cerebellum	SCAN
rs12337739	KIAA1958	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117662200-117676200	Weak transcription	Gastric	stomach
2	chr9:117663400-117672800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr9:117663600-117672400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr9:117665600-117671000	Weak transcription	NHLF	lung
5	chr9:117665800-117672800	Weak transcription	Spleen	Spleen
6	chr9:117667400-117673600	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr9:117667600-117673200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:117667800-117683600	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr9:117668600-117671800	Enhancers	Placenta	Placenta
10	chr9:117668600-117672000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr9:117668800-117673400	Enhancers	Primary B cells from peripheral blood	blood
12	chr9:117668800-117673400	Enhancers	HMEC	breast
13	chr9:117669000-117671800	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr9:117669000-117672200	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr9:117669000-117674000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr9:117669200-117670800	Enhancers	Primary T cells from cord blood	blood
17	chr9:117669200-117671200	Genic enhancers	Thymus	Thymus
18	chr9:117669200-117671400	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr9:117669200-117671600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr9:117669200-117671600	Enhancers	Placenta Amnion	Placenta Amnion
21	chr9:117669200-117671600	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr9:117669200-117672000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr9:117669200-117672000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr9:117669200-117672200	Enhancers	Fetal Lung	lung
25	chr9:117669200-117673200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr9:117669200-117673800	Enhancers	Fetal Thymus	thymus
27	chr9:117669400-117670800	Enhancers	Hela-S3	cervix
28	chr9:117669400-117670800	Enhancers	HSMM	muscle
29	chr9:117669400-117671000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr9:117669400-117671400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr9:117669400-117671400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr9:117669400-117671400	Enhancers	Lung	lung
33	chr9:117669400-117671600	Enhancers	NHEK	skin
34	chr9:117669400-117671800	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr9:117669400-117671800	Enhancers	HepG2	liver
36	chr9:117669400-117672400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
37	chr9:117669600-117670800	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr9:117669600-117671200	Enhancers	Liver	Liver
39	chr9:117669600-117671400	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr9:117669600-117671600	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr9:117669600-117671600	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr9:117669600-117671600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr9:117669600-117671800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr9:117669800-117670800	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr9:117669800-117671800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr9:117669800-117672600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr9:117669800-117672800	Weak transcription	Fetal Stomach	stomach
48	chr9:117669800-117673600	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr9:117670000-117670800	Enhancers	Primary B cells from cord blood	blood
50	chr9:117670000-117671000	Weak transcription	Pancreas	Pancrea

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