Variant report

Variant	rs690304
Chromosome Location	chr9:98644236-98644237
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98643243..98646230-chr9:98646548..98650436,4	MCF-7	breast:
2	chr9:98642876..98646721-chr9:98647995..98651810,4	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10121403	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10481647	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739632	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760675	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10760692	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10818017	0.82[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10983622	0.81[CHB][hapmap];0.82[EUR][1000 genomes]
rs10983692	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10983739	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10983773	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10983818	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12004422	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12375861	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12553442	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1410783	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1928253	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2117432	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2164156	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2164157	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs238	0.92[CEU][hapmap]
rs2770837	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3930253	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4743458	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs583716	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs585223	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs591579	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs601916	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs615866	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs617884	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs626264	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs631273	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs636456	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs640281	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs643815	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6478984	0.84[ASN][1000 genomes]
rs6479036	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs676453	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs678244	0.96[CEU][hapmap]
rs680468	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs680754	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs683829	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs689627	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs689749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs689820	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs689871	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs689979	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs690222	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs690335	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs690420	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs690455	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs690484	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs700963	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7024710	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7028281	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7868559	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7874897	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs816671	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs816676	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs816681	0.86[ASN][1000 genomes]
rs913408	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9409321	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9409322	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	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
4	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs690304	LINC00476	cis	Thyroid	GTEx
rs690304	LINC00476	cis	Nerve Tibial	GTEx
rs690304	LINC00476	cis	Skin Sun Exposed Lower leg	GTEx
rs690304	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs690304	LINC00476	cis	Artery Aorta	GTEx
rs690304	LINC00476	cis	Stomach	GTEx
rs690304	LINC00476	cis	lung	GTEx
rs690304	LINC00476	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98638800-98648000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:98638800-98648400	Weak transcription	Lung	lung
3	chr9:98638800-98649000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:98638800-98654800	Weak transcription	Esophagus	oesophagus
5	chr9:98638800-98702200	Weak transcription	Pancreas	Pancrea
6	chr9:98639400-98647800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:98639400-98649000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr9:98639400-98650800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr9:98639400-98677800	Weak transcription	Placenta	Placenta
10	chr9:98639400-98678000	Weak transcription	Ovary	ovary
11	chr9:98639600-98644600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr9:98639600-98646200	Weak transcription	HSMMtube	muscle
13	chr9:98639600-98649200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr9:98639600-98678000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr9:98639800-98664200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr9:98639800-98677800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr9:98640000-98644400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr9:98640000-98645400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr9:98640000-98649000	Weak transcription	Spleen	Spleen
20	chr9:98640000-98661600	Weak transcription	Right Atrium	heart
21	chr9:98640000-98663600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr9:98640000-98678200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr9:98640000-98680600	Weak transcription	Colonic Mucosa	Colon
24	chr9:98640000-98685600	Weak transcription	Right Ventricle	heart
25	chr9:98640000-98718600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr9:98640200-98678200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr9:98640400-98644400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr9:98640400-98649200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr9:98640400-98664800	Weak transcription	Brain Substantia Nigra	brain
30	chr9:98640400-98677800	Weak transcription	Psoas Muscle	Psoas
31	chr9:98640600-98647800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr9:98640600-98649000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr9:98640600-98678000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr9:98641400-98646400	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr9:98641600-98650000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr9:98642000-98647200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr9:98642000-98647600	Weak transcription	Fetal Brain Male	brain
38	chr9:98642200-98647600	Weak transcription	Fetal Heart	heart
39	chr9:98642200-98652400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr9:98642200-98654600	Weak transcription	Fetal Intestine Small	intestine
41	chr9:98642200-98663600	Weak transcription	Hela-S3	cervix
42	chr9:98642600-98645000	Weak transcription	NHDF-Ad	bronchial
43	chr9:98642600-98678000	Weak transcription	Colon Smooth Muscle	Colon
44	chr9:98642600-98680600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr9:98642800-98668200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr9:98642800-98681800	Weak transcription	Fetal Kidney	kidney
47	chr9:98643000-98645000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:98643000-98645800	Weak transcription	NH-A	brain
49	chr9:98643000-98648400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr9:98643200-98644600	Strong transcription	Primary monocytes fromperipheralblood	blood

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