Variant report

Variant	rs601916
Chromosome Location	chr9:98718533-98718534
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10121403	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10481647	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10739632	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10760675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10760692	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10818017	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs10983622	0.81[AMR][1000 genomes]
rs10983692	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs10983739	0.93[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs10983773	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs10983818	0.93[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes]
rs12004422	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12375861	0.89[ASW][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap];0.81[AMR][1000 genomes]
rs12553442	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1410783	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1928253	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2117432	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2164156	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2164157	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs238	0.96[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs2770837	0.85[AMR][1000 genomes]
rs3930253	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4743458	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs583716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs585223	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs591579	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs615866	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs617884	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs626264	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs631273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs636456	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs640281	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs643815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6479036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs676453	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs678244	1.00[CEU][hapmap]
rs680468	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs680754	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs683829	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs689627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs689749	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs689820	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs689871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs689979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs690152	0.82[EUR][1000 genomes]
rs690222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs690304	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]
rs690335	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs690420	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs690455	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs690484	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs700963	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes]
rs7024710	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7028281	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7868559	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7874897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs816671	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs816676	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes]
rs913408	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9409321	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs9409322	0.93[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv1035723	chr9:98701628-98734356	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs601916	LINC00476	cis	Stomach	GTEx
rs601916	C9orf130	cis	parietal	SCAN
rs601916	LINC00476	cis	lung	GTEx
rs601916	LINC00476	cis	Artery Aorta	GTEx
rs601916	LINC00476	cis	Thyroid	GTEx
rs601916	LINC00476	cis	Nerve Tibial	GTEx
rs601916	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs601916	LINC00476	cis	Adipose Subcutaneous	GTEx
rs601916	PTPDC1	cis	parietal	SCAN
rs601916	C9orf130	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98640000-98718600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:98649400-98718600	Weak transcription	Spleen	Spleen
3	chr9:98675400-98718600	Weak transcription	Esophagus	oesophagus
4	chr9:98678800-98718600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:98681800-98736600	Weak transcription	Colonic Mucosa	Colon
6	chr9:98686400-98743800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr9:98687800-98726000	Weak transcription	Gastric	stomach
8	chr9:98695800-98742400	Weak transcription	NHLF	lung
9	chr9:98699800-98718600	Weak transcription	NHEK	skin
10	chr9:98702400-98718600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr9:98702400-98718600	Weak transcription	Small Intestine	intestine
12	chr9:98702600-98718600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr9:98702600-98718600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:98702600-98718600	Weak transcription	Aorta	Aorta
15	chr9:98702600-98718600	Weak transcription	Pancreas	Pancrea
16	chr9:98705000-98718600	Weak transcription	K562	blood
17	chr9:98705000-98718800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr9:98705400-98734200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr9:98706400-98777400	Weak transcription	Psoas Muscle	Psoas
20	chr9:98706800-98734000	Weak transcription	Hela-S3	cervix
21	chr9:98709600-98718600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr9:98709800-98718600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr9:98709800-98718600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr9:98709800-98718600	Weak transcription	Left Ventricle	heart
25	chr9:98709800-98718800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr9:98709800-98718800	Weak transcription	Right Ventricle	heart
27	chr9:98709800-98727800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr9:98710000-98718600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr9:98710000-98718600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr9:98710000-98718600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr9:98710000-98718600	Weak transcription	Brain Angular Gyrus	brain
32	chr9:98710000-98718600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr9:98710000-98718600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr9:98710000-98719200	Weak transcription	Colon Smooth Muscle	Colon
35	chr9:98710000-98720000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr9:98710000-98734200	Weak transcription	HMEC	breast
37	chr9:98710000-98735000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr9:98710400-98718600	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr9:98710400-98741400	Weak transcription	Brain Anterior Caudate	brain
40	chr9:98711000-98718600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr9:98711000-98718600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr9:98711000-98718600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr9:98711000-98722000	Weak transcription	Brain Germinal Matrix	brain
44	chr9:98711000-98743400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr9:98711400-98718600	Weak transcription	Primary B cells from peripheral blood	blood
46	chr9:98711800-98718600	Weak transcription	Fetal Muscle Leg	muscle
47	chr9:98712000-98718600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr9:98712400-98718600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr9:98713800-98718600	Weak transcription	Fetal Brain Male	brain
50	chr9:98714000-98782600	Weak transcription	HUVEC	blood vessel

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