Variant report

Variant	rs11793856
Chromosome Location	chr9:96714491-96714492
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	SUZ12	chr9:96709708-96717433	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTBP2	chr9:96710652-96717425	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:96713619..96716485-chr9:96717370..96719166,2	K562	blood:
2	chr9:96710465..96712948-chr9:96713592..96715312,2	MCF-7	breast:
3	chr9:96709646..96715968-chr9:96715980..96721050,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235601	TF binding region
ENSG00000235601	Chromatin interaction
ENSG00000131668	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10993017	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10993047	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11788160	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11788176	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11789015	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11789837	0.86[CEU][hapmap]
rs11792744	1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11999153	0.83[CEU][hapmap]
rs12001386	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12004383	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs12684081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411861	0.95[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1539282	0.86[CEU][hapmap]
rs2039313	0.82[CEU][hapmap]
rs2095777	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2153791	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2398893	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34849895	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35480828	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35886839	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3909256	0.90[CEU][hapmap]
rs4316201	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5014099	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55947603	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56285369	0.84[EUR][1000 genomes]
rs56335449	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62574323	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62574346	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7047684	0.82[CEU][hapmap]
rs7849645	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7858520	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7872984	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893589	chr9:96624645-96884544	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv824993	chr9:96699362-96725105	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv893590	chr9:96701287-96729129	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96711600-96715600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
2	chr9:96712800-96714800	Bivalent/Poised TSS	HSMM	muscle
3	chr9:96713000-96714600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
4	chr9:96713000-96714800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr9:96713000-96715800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
6	chr9:96713000-96717000	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
7	chr9:96713200-96714600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr9:96713200-96714600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr9:96713200-96715000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr9:96713200-96715000	Bivalent Enhancer	Fetal Heart	heart
11	chr9:96713200-96716400	Bivalent Enhancer	Fetal Brain Male	brain
12	chr9:96713400-96714600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
13	chr9:96713400-96714800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
14	chr9:96713600-96714600	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
15	chr9:96713600-96716400	Weak transcription	Hela-S3	cervix
16	chr9:96713800-96714600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
17	chr9:96713800-96714600	Bivalent Enhancer	Stomach Mucosa	stomach
18	chr9:96713800-96715000	Bivalent Enhancer	Fetal Intestine Small	intestine
19	chr9:96713800-96715200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr9:96713800-96715200	Bivalent Enhancer	Fetal Intestine Large	intestine
21	chr9:96713800-96715200	Bivalent Enhancer	Placenta	Placenta
22	chr9:96713800-96715800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr9:96713800-96715800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
24	chr9:96713800-96716000	Bivalent Enhancer	Fetal Lung	lung
25	chr9:96713800-96716400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
26	chr9:96713800-96716600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
27	chr9:96713800-96716800	Bivalent Enhancer	Brain Germinal Matrix	brain
28	chr9:96713800-96716800	Bivalent Enhancer	Brain Substantia Nigra	brain
29	chr9:96713800-96717000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
30	chr9:96713800-96717200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
31	chr9:96713800-96717400	Bivalent Enhancer	Fetal Muscle Leg	muscle
32	chr9:96713800-96717800	Bivalent Enhancer	Liver	Liver
33	chr9:96713800-96718400	Bivalent Enhancer	Lung	lung
34	chr9:96714000-96714600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
35	chr9:96714000-96714600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
36	chr9:96714000-96714600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr9:96714000-96714600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr9:96714000-96714600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr9:96714000-96714600	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
40	chr9:96714000-96714600	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
41	chr9:96714000-96714600	Bivalent Enhancer	NH-A	brain
42	chr9:96714000-96714800	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
43	chr9:96714000-96714800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr9:96714000-96714800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:96714000-96714800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
46	chr9:96714000-96714800	Bivalent Enhancer	Spleen	Spleen
47	chr9:96714000-96715000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
48	chr9:96714000-96715000	Strong transcription	Osteobl	bone
49	chr9:96714000-96715200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
50	chr9:96714200-96714600	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood

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