Variant report

Variant	rs11789015
Chromosome Location	chr9:96716028-96716029
allele	A/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	POLR2A	chr9:96715218-96716678	H1-neurons	neurons:	n/a	n/a
3	CTBP2	chr9:96710652-96717425	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr9:96715057-96716383	H1-neurons	neurons:	n/a	n/a

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

Variant related genes	Relation type
BARX1	TF binding region
ENSG00000235601	TF binding region
ENSG00000131668	Chromatin interaction
ENSG00000235601	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10821274	0.87[AFR][1000 genomes]
rs10993017	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10993047	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs11788035	0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs11788160	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11788176	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11789837	0.83[CEU][hapmap]
rs11792744	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11793856	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]
rs12001386	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12004383	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12684081	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13283836	0.86[AFR][1000 genomes]
rs1411861	0.91[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes]
rs1539282	0.83[CEU][hapmap]
rs1933680	0.85[AFR][1000 genomes]
rs1933681	0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs2095777	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2153791	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2398893	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34849895	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35001304	0.83[AFR][1000 genomes]
rs35480828	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35886839	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3909256	0.83[CEU][hapmap]
rs4316201	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5014099	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55947603	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56285369	0.85[EUR][1000 genomes]
rs56335449	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62574323	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62574346	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7034685	0.85[AFR][1000 genomes]
rs7849645	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7858520	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

Variant related diseases (count:3)

Disease	PMID	Source
Barrett's esophagus	24121790	GWAS catalog
Esophageal adenocarcinoma	24121790	GWAS catalog
Digestive system disease (Barrett's esophagus and esophageal adenocarcinoma combined)	24121790	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11789015	C9orf3	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96713000-96717000	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
2	chr9:96713200-96716400	Bivalent Enhancer	Fetal Brain Male	brain
3	chr9:96713600-96716400	Weak transcription	Hela-S3	cervix
4	chr9:96713800-96716400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
5	chr9:96713800-96716600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
6	chr9:96713800-96716800	Bivalent Enhancer	Brain Germinal Matrix	brain
7	chr9:96713800-96716800	Bivalent Enhancer	Brain Substantia Nigra	brain
8	chr9:96713800-96717000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr9:96713800-96717200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
10	chr9:96713800-96717400	Bivalent Enhancer	Fetal Muscle Leg	muscle
11	chr9:96713800-96717800	Bivalent Enhancer	Liver	Liver
12	chr9:96713800-96718400	Bivalent Enhancer	Lung	lung
13	chr9:96714200-96716200	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
14	chr9:96714200-96716400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
15	chr9:96714200-96716600	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr9:96714200-96717200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
17	chr9:96714200-96717400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
18	chr9:96714200-96717800	Enhancers	Pancreas	Pancrea
19	chr9:96714400-96716200	Bivalent Enhancer	Brain Cingulate Gyrus	brain
20	chr9:96714400-96717000	Bivalent Enhancer	Adipose Nuclei	Adipose
21	chr9:96714400-96717200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
22	chr9:96714600-96716400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
23	chr9:96714600-96716800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
24	chr9:96714600-96716800	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
25	chr9:96714600-96717000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
26	chr9:96714600-96717000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr9:96714600-96717000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:96714800-96716200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
29	chr9:96714800-96716800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
30	chr9:96715000-96716200	Weak transcription	Osteobl	bone
31	chr9:96715000-96716400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
32	chr9:96715000-96716400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr9:96715000-96717000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
34	chr9:96715000-96718800	Bivalent Enhancer	Spleen	Spleen
35	chr9:96715200-96716200	Bivalent/Poised TSS	Fetal Stomach	stomach
36	chr9:96715400-96716200	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
37	chr9:96715400-96716600	Bivalent Enhancer	Colonic Mucosa	Colon
38	chr9:96715400-96716800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
39	chr9:96715400-96717200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
40	chr9:96715600-96716400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
41	chr9:96715800-96716200	Bivalent Enhancer	Colon Smooth Muscle	Colon
42	chr9:96715800-96716200	Active TSS	Gastric	stomach
43	chr9:96715800-96716400	Bivalent Enhancer	Fetal Heart	heart
44	chr9:96715800-96716400	Bivalent Enhancer	Right Ventricle	heart
45	chr9:96715800-96716600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr9:96715800-96717000	Bivalent Enhancer	Brain Hippocampus Middle	brain
47	chr9:96715800-96717000	Weak transcription	Right Atrium	heart
48	chr9:96715800-96717200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr9:96715800-96717200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr9:96716000-96716200	Bivalent Enhancer	Fetal Brain Female	brain

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