Variant report

Variant	rs4743436
Chromosome Location	chr9:98737537-98737538
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98735548..98738527-chr9:98741543..98743511,2	K562	blood:
2	chr9:98735212..98738334-chr9:98738924..98741955,4	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10983321	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs10988581	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10988804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11787559	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11790370	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11790491	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11793298	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11794054	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12683634	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12685221	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12686222	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12686457	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1360064	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16910262	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16910296	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16910298	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16910418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1831228	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1999023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2026032	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2069053	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34533243	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3780574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4532708	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4742775	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4742781	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4743372	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4743418	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743472	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7048414	0.90[CEU][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes]
rs73536517	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73656544	0.82[EUR][1000 genomes]
rs7868270	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[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	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS 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	52 gene(s)	inside rSNPs	diseases
2	nsv893600	chr9:98608989-98775459	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4743436	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs4743436	LINC00476	cis	Whole Blood	GTEx
rs4743436	LINC00476	cis	Esophagus Mucosa	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98686400-98743800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr9:98695800-98742400	Weak transcription	NHLF	lung
3	chr9:98706400-98777400	Weak transcription	Psoas Muscle	Psoas
4	chr9:98710400-98741400	Weak transcription	Brain Anterior Caudate	brain
5	chr9:98711000-98743400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr9:98714000-98782600	Weak transcription	HUVEC	blood vessel
7	chr9:98719000-98738600	Weak transcription	Aorta	Aorta
8	chr9:98719000-98743800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr9:98719000-98751400	Weak transcription	Stomach Mucosa	stomach
10	chr9:98719200-98744000	Weak transcription	Brain Substantia Nigra	brain
11	chr9:98719200-98744400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr9:98719200-98749600	Weak transcription	Fetal Intestine Small	intestine
13	chr9:98719200-98749800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:98719200-98752800	Weak transcription	Pancreas	Pancrea
15	chr9:98719200-98764200	Weak transcription	Spleen	Spleen
16	chr9:98719200-98767800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr9:98719400-98742800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr9:98719400-98744000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr9:98719400-98744000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr9:98719400-98767200	Weak transcription	Right Ventricle	heart
21	chr9:98719400-98771000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr9:98719600-98743800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr9:98719600-98766800	Weak transcription	Colon Smooth Muscle	Colon
24	chr9:98722400-98747800	Weak transcription	Fetal Heart	heart
25	chr9:98723800-98749800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr9:98725400-98743600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:98726400-98767800	Weak transcription	Gastric	stomach
28	chr9:98730000-98744400	Weak transcription	Fetal Stomach	stomach
29	chr9:98730600-98751200	Weak transcription	Small Intestine	intestine
30	chr9:98732200-98747400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr9:98732200-98751200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr9:98732600-98741000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr9:98733000-98737600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr9:98733000-98749600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr9:98733800-98737600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr9:98733800-98737600	Strong transcription	Fetal Thymus	thymus
37	chr9:98734400-98739200	Weak transcription	Esophagus	oesophagus
38	chr9:98734600-98742600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:98734600-98742600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr9:98734600-98744000	Weak transcription	Brain Angular Gyrus	brain
41	chr9:98734600-98749800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr9:98734600-98764400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr9:98734600-98767800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr9:98734600-98782400	Weak transcription	NHEK	skin
45	chr9:98734800-98737600	Strong transcription	Fetal Kidney	kidney
46	chr9:98735000-98742600	Weak transcription	Brain Germinal Matrix	brain
47	chr9:98735200-98740200	Weak transcription	Primary B cells from peripheral blood	blood
48	chr9:98735200-98742400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr9:98735200-98742600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr9:98735200-98751600	Weak transcription	NHDF-Ad	bronchial

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