Variant report

Variant	rs7020644
Chromosome Location	chr9:100665624-100665625
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100663583..100665725-chr9:100672529..100674637,2	K562	blood:
2	chr9:100665233..100671095-chr9:100679720..100686341,8	MCF-7	breast:
3	chr9:100657173..100659801-chr9:100665045..100666603,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136932	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10113907	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10119795	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10818239	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11999801	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12003789	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12238579	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13300874	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13301569	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1561958	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1561959	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2120263	0.81[AMR][1000 genomes]
rs4743140	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6478450	0.86[EUR][1000 genomes]
rs6586	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67449879	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7033315	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7357707	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7853349	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7870125	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs874004	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7020644	C9orf156	cis	Skin Sun Exposed Lower leg	GTEx
rs7020644	FOXE1	cis	Esophagus Mucosa	GTEx
rs7020644	C9orf156	cis	Esophagus Mucosa	GTEx
rs7020644	C9orf156	cis	Esophagus Muscularis	GTEx
rs7020644	C9orf156	cis	Thyroid	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100652800-100666600	Weak transcription	Fetal Lung	lung
2	chr9:100653000-100667000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:100654200-100666600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr9:100656000-100667600	Weak transcription	Fetal Muscle Leg	muscle
5	chr9:100656000-100669400	Weak transcription	Brain Substantia Nigra	brain
6	chr9:100656200-100666800	Weak transcription	Brain Germinal Matrix	brain
7	chr9:100656200-100670400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr9:100656400-100668400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr9:100656400-100669800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr9:100656400-100669800	Weak transcription	Fetal Brain Female	brain
11	chr9:100656600-100667000	Weak transcription	Brain Anterior Caudate	brain
12	chr9:100656800-100666800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr9:100656800-100668400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr9:100656800-100669400	Weak transcription	Left Ventricle	heart
15	chr9:100656800-100672400	Weak transcription	Stomach Mucosa	stomach
16	chr9:100657000-100666600	Weak transcription	Placenta	Placenta
17	chr9:100657000-100669400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr9:100657000-100669400	Weak transcription	Right Ventricle	heart
19	chr9:100658200-100671600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr9:100658400-100669400	Weak transcription	Hela-S3	cervix
21	chr9:100658400-100671600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr9:100658600-100666600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr9:100658600-100666800	Weak transcription	Pancreas	Pancrea
24	chr9:100658600-100667600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr9:100658600-100669400	Weak transcription	Gastric	stomach
26	chr9:100658600-100671600	Weak transcription	Ovary	ovary
27	chr9:100658600-100671600	Weak transcription	Small Intestine	intestine
28	chr9:100658600-100672200	Weak transcription	Esophagus	oesophagus
29	chr9:100658800-100681800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr9:100660200-100671200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr9:100660600-100668400	Weak transcription	Brain Hippocampus Middle	brain
32	chr9:100660800-100669400	Weak transcription	Aorta	Aorta
33	chr9:100661000-100666400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr9:100661200-100669800	Weak transcription	K562	blood
35	chr9:100662000-100667400	Strong transcription	Primary B cells from peripheral blood	blood
36	chr9:100662400-100666800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr9:100662400-100667200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr9:100662600-100666600	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr9:100662600-100666800	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr9:100662800-100666600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr9:100662800-100666600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr9:100662800-100666600	Weak transcription	Fetal Muscle Trunk	muscle
43	chr9:100662800-100667000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr9:100662800-100669400	Weak transcription	Lung	lung
45	chr9:100662800-100684200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr9:100663000-100666200	Weak transcription	Duodenum Mucosa	Duodenum
47	chr9:100663000-100666400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr9:100663000-100666800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr9:100663000-100666800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr9:100663000-100666800	Weak transcription	Fetal Stomach	stomach

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