Variant report

Variant	rs626264
Chromosome Location	chr9:98737329-98737330
allele	A/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: 56 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10121403	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10481647	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10739632	0.88[AMR][1000 genomes]
rs10739787	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10760675	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10760692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818017	0.80[AMR][1000 genomes]
rs10983622	0.80[AMR][1000 genomes]
rs10983692	0.80[AMR][1000 genomes]
rs10983818	0.80[AMR][1000 genomes]
rs12004422	0.92[CEU][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12375861	0.80[AMR][1000 genomes]
rs12553442	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1928253	0.81[AMR][1000 genomes]
rs2164157	0.80[AMR][1000 genomes]
rs238	0.96[CEU][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes]
rs2770837	0.84[AMR][1000 genomes]
rs3930253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743458	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs583716	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs585223	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs601916	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs615866	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs617884	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs631273	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs636456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs640281	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs643815	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6479036	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs676453	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs678244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs680468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs680754	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs689627	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs689749	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs689820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689871	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs689979	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs690152	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs690222	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs690304	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs690335	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs690420	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs690455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs690484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs700963	0.81[AMR][1000 genomes]
rs7024710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7028281	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7868559	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7874897	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs816676	0.81[AMR][1000 genomes]
rs913408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9409321	0.84[AMR][1000 genomes]
rs9409322	0.84[AMR][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs626264	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs626264	LINC00476	cis	Adipose Subcutaneous	GTEx
rs626264	LINC00476	cis	Artery Aorta	GTEx
rs626264	LINC00476	cis	Skin Sun Exposed Lower leg	GTEx
rs626264	LINC00476	cis	Thyroid	GTEx
rs626264	LINC00476	cis	lung	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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