Variant report

Variant	rs4743458
Chromosome Location	chr9:98767640-98767641
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98753369..98756091-chr9:98765183..98768443,3	K562	blood:
2	chr9:98758966..98761197-chr9:98765461..98768218,3	K562	blood:
3	chr9:98758267..98760888-chr9:98765461..98767832,3	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	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10481647	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10739632	0.80[AMR][1000 genomes]
rs10739787	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10760675	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10760692	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]
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	0.84[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12375861	0.80[AMR][1000 genomes]
rs12553442	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1928253	0.81[AMR][1000 genomes]
rs2164157	0.80[AMR][1000 genomes]
rs238	0.88[CEU][hapmap];0.92[JPT][hapmap];0.89[EUR][1000 genomes]
rs2770837	0.84[AMR][1000 genomes]
rs3930253	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs583716	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs585223	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs601916	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs615866	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs617884	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs626264	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]
rs631273	0.92[CEU][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs636456	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs640281	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs643815	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6479036	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs676453	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678244	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs680468	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680754	0.92[CEU][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs689627	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs689749	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs689820	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs689871	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs689979	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs690152	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs690222	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs690304	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs690335	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs690420	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs690455	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690484	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs700963	0.81[AMR][1000 genomes]
rs7024710	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7028281	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7868559	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7874897	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs816676	0.81[AMR][1000 genomes]
rs913408	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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
rs4743458	LINC00476	cis	Nerve Tibial	GTEx
rs4743458	LINC00476	cis	Adipose Subcutaneous	GTEx
rs4743458	LINC00476	cis	Artery Aorta	GTEx
rs4743458	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs4743458	LINC00476	cis	lung	GTEx
rs4743458	LINC00476	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98706400-98777400	Weak transcription	Psoas Muscle	Psoas
2	chr9:98714000-98782600	Weak transcription	HUVEC	blood vessel
3	chr9:98719200-98767800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr9:98719400-98771000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr9:98726400-98767800	Weak transcription	Gastric	stomach
6	chr9:98734600-98767800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr9:98734600-98782400	Weak transcription	NHEK	skin
8	chr9:98735400-98778400	Weak transcription	Hela-S3	cervix
9	chr9:98735800-98770600	Weak transcription	K562	blood
10	chr9:98735800-98771200	Weak transcription	HepG2	liver
11	chr9:98736600-98778800	Weak transcription	Fetal Brain Male	brain
12	chr9:98741800-98778600	Weak transcription	NH-A	brain
13	chr9:98744600-98768000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr9:98744800-98770800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr9:98744800-98771000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr9:98747800-98782800	Weak transcription	Fetal Kidney	kidney
17	chr9:98748000-98782600	Weak transcription	HMEC	breast
18	chr9:98748200-98771000	Weak transcription	Fetal Heart	heart
19	chr9:98748400-98767800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr9:98748400-98767800	Weak transcription	NHLF	lung
21	chr9:98748400-98768400	Weak transcription	HSMMtube	muscle
22	chr9:98748400-98770600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr9:98748400-98782800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr9:98748600-98781200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr9:98749400-98770800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr9:98749600-98770200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr9:98750400-98768200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr9:98750400-98768400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr9:98750400-98771400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr9:98750400-98771400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:98750800-98771000	Weak transcription	A549	lung
32	chr9:98751600-98767800	Weak transcription	Colonic Mucosa	Colon
33	chr9:98751600-98772600	Weak transcription	Small Intestine	intestine
34	chr9:98751800-98767800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr9:98752400-98768600	Weak transcription	Osteobl	bone
36	chr9:98753400-98768400	Weak transcription	Left Ventricle	heart
37	chr9:98753400-98774200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr9:98753600-98768400	Weak transcription	Brain Hippocampus Middle	brain
39	chr9:98753600-98768600	Weak transcription	Esophagus	oesophagus
40	chr9:98753600-98769000	Weak transcription	Pancreas	Pancrea
41	chr9:98753600-98774400	Weak transcription	Brain Anterior Caudate	brain
42	chr9:98753800-98767800	Weak transcription	Brain Angular Gyrus	brain
43	chr9:98753800-98768400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr9:98754000-98767800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr9:98754000-98767800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr9:98754600-98770200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr9:98755800-98767800	Weak transcription	Ovary	ovary
48	chr9:98756000-98768600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr9:98757000-98768400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr9:98757000-98770800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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