Variant report

Variant	rs9450630
Chromosome Location	chr6:87899160-87899161
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1145712	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1145713	0.82[EUR][1000 genomes]
rs1145714	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1145715	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11759727	0.84[EUR][1000 genomes]
rs1188816	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1188817	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1188819	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs1203162	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1203163	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1203164	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12211627	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13201289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13210074	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16878497	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1739886	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1746444	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1753152	0.87[CEU][hapmap]
rs1925686	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1925689	0.83[CEU][hapmap]
rs2025490	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2147917	0.84[CEU][hapmap]
rs2147918	0.83[CEU][hapmap]
rs242263	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs242264	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs242265	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs242268	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs242269	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs242275	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs242276	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs242282	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2983136	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs368267	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs3734187	0.83[CEU][hapmap]
rs374792	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs377288	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs379455	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3812130	0.83[CEU][hapmap]
rs381798	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs382956	0.81[EUR][1000 genomes]
rs384318	0.82[EUR][1000 genomes]
rs3846776	0.83[CEU][hapmap]
rs3857483	0.87[CEU][hapmap]
rs3857484	0.84[CEU][hapmap]
rs3857486	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs397516	0.90[CHB][hapmap]
rs398140	0.89[JPT][hapmap]
rs3999791	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs406981	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4099964	0.84[CEU][hapmap]
rs410683	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs411606	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs413687	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs414453	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs4235830	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs440296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs452315	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4707344	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4707345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4707348	0.84[CEU][hapmap]
rs4707355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs540975	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs541170	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6454593	0.82[CEU][hapmap]
rs6907805	0.83[CEU][hapmap]
rs6908834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs6913159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913932	0.84[CEU][hapmap]
rs6921007	0.83[CEU][hapmap]
rs6921673	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6926686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs6927748	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs6932641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6933046	0.83[CEU][hapmap]
rs6934603	0.83[CEU][hapmap]
rs6938885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs6939075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs6940325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6940544	0.83[CEU][hapmap]
rs7752414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7755883	0.83[CEU][hapmap]
rs7757330	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7758360	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7767245	0.86[EUR][1000 genomes]
rs7774603	0.83[CEU][hapmap]
rs910564	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs912815	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9294375	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9294376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs9344691	0.84[CEU][hapmap]
rs9344695	0.83[CEU][hapmap]
rs9353468	0.83[CEU][hapmap]
rs9359743	0.83[CEU][hapmap]
rs9362411	0.84[CEU][hapmap]
rs9362415	0.83[CEU][hapmap]
rs9444476	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9444481	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9444486	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9444488	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9444490	0.86[EUR][1000 genomes]
rs9444491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs9450619	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9450623	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9450636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450637	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9450638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9450639	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9450640	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450646	0.86[EUR][1000 genomes]
rs9450650	0.83[CEU][hapmap]
rs9450651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs9450652	0.84[CEU][hapmap]
rs9450653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][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	nsv1024751	chr6:87433199-87908721	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription 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	27 gene(s)	inside rSNPs	diseases
2	nsv604114	chr6:87816905-87906053	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2758067	chr6:87817883-87992957	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv2759453	chr6:87817883-87992957	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9450630	Hs.485895	cis	multi-tissue	Pritchard
rs9450630	C6orf163	Cis_1M	lymphoblastoid	RTeQTL
rs9450630	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs9450630	C6orf162	cis	multi-tissue	Pritchard
rs9450630	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87867000-87915600	Weak transcription	NH-A	brain
2	chr6:87868000-87933000	Weak transcription	Hela-S3	cervix
3	chr6:87874400-87924200	Weak transcription	Fetal Kidney	kidney
4	chr6:87875000-87910400	Weak transcription	K562	blood
5	chr6:87879800-87923000	Weak transcription	Esophagus	oesophagus
6	chr6:87880600-87906000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:87881400-87926200	Weak transcription	Liver	Liver
8	chr6:87881800-87909400	Weak transcription	Fetal Brain Male	brain
9	chr6:87882000-87899400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr6:87883400-87926200	Weak transcription	Fetal Lung	lung
11	chr6:87884000-87906000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:87884000-87964400	Weak transcription	NHEK	skin
13	chr6:87884600-87899400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr6:87888200-87964200	Weak transcription	HSMMtube	muscle
15	chr6:87889800-87926400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:87890200-87905800	Weak transcription	Brain Hippocampus Middle	brain
17	chr6:87890200-87906000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr6:87890200-87909400	Weak transcription	Brain Substantia Nigra	brain
19	chr6:87890800-87909600	Weak transcription	Brain Germinal Matrix	brain
20	chr6:87890800-87910000	Weak transcription	Right Ventricle	heart
21	chr6:87890800-87933000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:87891000-87902800	Weak transcription	Pancreas	Pancrea
23	chr6:87891000-87920000	Weak transcription	Placenta	Placenta
24	chr6:87891000-87956000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:87891200-87913000	Weak transcription	Lung	lung
26	chr6:87891200-87929200	Weak transcription	Thymus	Thymus
27	chr6:87891400-87912800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:87891400-87932600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:87892000-87923000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr6:87892400-87899400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr6:87892800-87901200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr6:87892800-87921600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr6:87893000-87917600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr6:87893800-87915600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr6:87894000-87915600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:87894800-87921800	Weak transcription	NHDF-Ad	bronchial
37	chr6:87894800-87924200	Weak transcription	Adipose Nuclei	Adipose
38	chr6:87894800-87926200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:87895400-87906200	Weak transcription	NHLF	lung
40	chr6:87895800-87902800	Weak transcription	Ovary	ovary
41	chr6:87895800-87903200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr6:87895800-87912600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr6:87895800-87924000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr6:87896000-87903000	Weak transcription	Left Ventricle	heart
45	chr6:87896000-87909600	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr6:87896000-87932800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr6:87896200-87920200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:87896200-87921400	Weak transcription	HepG2	liver
49	chr6:87896400-87903600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr6:87896400-87906000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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