Variant report

Variant	rs12685829
Chromosome Location	chr9:71801392-71801393
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71793437..71796575-chr9:71800849..71803990,3	MCF-7	breast:
2	chr9:71794571..71798394-chr9:71798897..71802534,4	K562	blood:
3	chr9:71793542..71796888-chr9:71798932..71802737,4	MCF-7	breast:
4	chr9:71800754..71805797-chr9:71805912..71810495,5	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10735655	0.87[CHB][hapmap]
rs10869992	0.87[CHB][hapmap]
rs10869993	0.87[CHB][hapmap]
rs10869994	0.87[CHB][hapmap]
rs10869997	0.86[CHB][hapmap]
rs11145460	0.80[CHB][hapmap]
rs11145501	0.89[ASN][1000 genomes]
rs17061543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17062126	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[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]
rs17062237	0.87[CHB][hapmap]
rs17062397	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2309422	0.87[CHB][hapmap]
rs2309425	0.87[CHB][hapmap]
rs2309426	0.93[CHB][hapmap]
rs2498428	0.81[JPT][hapmap]
rs2993820	0.87[CHB][hapmap]
rs3002379	0.85[CHB][hapmap]
rs3002382	0.87[CHB][hapmap]
rs4375066	0.87[CHB][hapmap]
rs4576478	0.87[CHB][hapmap]
rs4744837	0.83[ASN][1000 genomes]
rs4745646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs60996078	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7850766	0.87[CHB][hapmap]
rs7854933	0.88[ASN][1000 genomes]
rs7872806	0.84[ASN][1000 genomes]
rs867346	0.93[CHB][hapmap]
rs884428	0.87[CHB][hapmap]
rs884429	0.87[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1053402	chr9:71399722-71819949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv540146	chr9:71399722-71819949	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv1047540	chr9:71401918-71803639	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv1035823	chr9:71465139-71901672	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv466396	chr9:71471912-71935577	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv614548	chr9:71471912-71935577	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
11	nsv466397	chr9:71574757-71843023	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv614550	chr9:71574757-71843023	Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	nsv1050692	chr9:71578494-71843023	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	nsv893416	chr9:71597840-71888601	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
15	nsv1040539	chr9:71600042-71844108	Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
16	nsv540149	chr9:71600042-71844108	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
17	nsv949664	chr9:71607398-71842391	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
18	nsv948708	chr9:71632265-71842391	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
19	nsv1037787	chr9:71635338-71807648	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
20	nsv540151	chr9:71635338-71807648	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
21	nsv817209	chr9:71675454-71829412	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
22	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
23	nsv508550	chr9:71679166-71809433	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
24	nsv893427	chr9:71762766-71858517	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71790400-71832200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr9:71790400-71835600	Weak transcription	Colonic Mucosa	Colon
3	chr9:71790800-71802200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:71791200-71802000	Weak transcription	Aorta	Aorta
5	chr9:71791200-71807600	Weak transcription	Psoas Muscle	Psoas
6	chr9:71791400-71804400	Enhancers	Placenta Amnion	Placenta Amnion
7	chr9:71792200-71801400	Weak transcription	Fetal Kidney	kidney
8	chr9:71792200-71802400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr9:71792400-71808800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:71793600-71805600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr9:71794000-71806000	Weak transcription	Primary T cells from cord blood	blood
12	chr9:71794200-71802400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr9:71795600-71814400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr9:71795800-71802600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr9:71795800-71804200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr9:71795800-71806400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr9:71796000-71801400	Weak transcription	HSMM	muscle
18	chr9:71796000-71802400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr9:71796000-71802600	Weak transcription	Gastric	stomach
20	chr9:71796000-71805600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr9:71797000-71801400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:71797000-71802400	Weak transcription	Left Ventricle	heart
23	chr9:71797000-71805800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr9:71797000-71814600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr9:71797200-71801400	Weak transcription	Hela-S3	cervix
26	chr9:71797200-71801400	Weak transcription	NHDF-Ad	bronchial
27	chr9:71797200-71802000	Weak transcription	Ovary	ovary
28	chr9:71797200-71802400	Weak transcription	Right Ventricle	heart
29	chr9:71797200-71804000	Weak transcription	Lung	lung
30	chr9:71797200-71805800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr9:71797200-71832000	Weak transcription	Esophagus	oesophagus
32	chr9:71797400-71801400	Weak transcription	GM12878-XiMat	blood
33	chr9:71797400-71802600	Weak transcription	Right Atrium	heart
34	chr9:71797600-71801400	Weak transcription	NHLF	lung
35	chr9:71797600-71802200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr9:71797600-71802800	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr9:71797800-71801800	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr9:71798400-71807400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr9:71798800-71801600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr9:71799200-71804600	Enhancers	Placenta	Placenta
41	chr9:71799600-71801400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr9:71799600-71801400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:71799600-71802200	Enhancers	HepG2	liver
44	chr9:71799600-71808400	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr9:71799800-71801800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr9:71800600-71806600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr9:71800800-71801600	Enhancers	Pancreas	Pancrea
48	chr9:71800800-71802600	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr9:71800800-71802600	Flanking Active TSS	K562	blood
50	chr9:71800800-71803200	Enhancers	HMEC	breast

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