Variant report

Variant	rs10038608
Chromosome Location	chr5:43462210-43462211
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:43460240..43463188-chr5:43481708..43484249,2	MCF-7	breast:
2	chr5:43442199..43444663-chr5:43460452..43462412,2	K562	blood:

Variant related genes	Relation type
ENSG00000249492	Chromatin interaction
ENSG00000151881	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10036954	0.92[CEU][hapmap];0.90[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10042992	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs10045400	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10045455	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10055801	0.91[MEX][hapmap]
rs10057103	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap]
rs10058558	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10059993	0.96[MEX][hapmap]
rs10061165	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10065689	0.96[MEX][hapmap]
rs10065863	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap]
rs10074682	0.96[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10447144	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10462051	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs10473311	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1072745	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1072746	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10941640	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11949083	0.96[MEX][hapmap]
rs12332560	0.82[EUR][1000 genomes]
rs12521249	0.96[MEX][hapmap]
rs12651879	0.82[EUR][1000 genomes]
rs12652547	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs12659369	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12697452	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13185343	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13189004	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1366410	0.96[MEX][hapmap]
rs1389868	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1389869	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1428640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2013173	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2131999	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2132000	0.94[EUR][1000 genomes]
rs2172763	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34007811	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35710460	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35881272	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36013953	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3776423	0.96[CEU][hapmap];0.90[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3806870	1.00[CEU][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4072918	0.96[MEX][hapmap]
rs4072919	0.91[MEX][hapmap]
rs4073848	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4073850	0.90[EUR][1000 genomes]
rs4073851	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4074777	0.96[MEX][hapmap]
rs4242099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4308491	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4331909	0.89[EUR][1000 genomes]
rs4367306	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4386738	0.96[MEX][hapmap]
rs4415083	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4467713	0.96[CEU][hapmap];0.90[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs4513704	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4535459	0.92[MEX][hapmap]
rs4541663	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4576155	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4866746	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4866752	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap]
rs4866833	0.96[CEU][hapmap];0.90[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs55641556	0.84[EUR][1000 genomes]
rs56400900	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs57547662	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57597020	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6451692	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6451693	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6451695	0.96[CEU][hapmap];0.90[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6451696	0.96[CEU][hapmap];0.90[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6451698	0.96[CEU][hapmap];0.83[MEX][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6451703	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6451704	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6451706	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6451712	0.83[EUR][1000 genomes]
rs6451718	0.87[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs67466542	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67581152	0.81[EUR][1000 genomes]
rs6858942	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6859344	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6860493	0.96[MEX][hapmap]
rs6861704	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6862102	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6865217	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6870018	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6870783	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6878770	0.96[MEX][hapmap]
rs6883661	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6884661	0.96[MEX][hapmap]
rs6885679	0.96[MEX][hapmap]
rs6895327	0.96[MEX][hapmap]
rs6896693	0.96[MEX][hapmap]
rs73100614	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs750582	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs750584	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7703662	0.94[JPT][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7707976	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7708369	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7708443	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7710628	0.92[MEX][hapmap]
rs7713479	0.96[MEX][hapmap]
rs7715782	0.96[MEX][hapmap]
rs7717636	0.82[EUR][1000 genomes]
rs7718627	0.96[MEX][hapmap]
rs7724571	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7731091	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7732656	0.96[MEX][hapmap]
rs7734393	0.84[EUR][1000 genomes]
rs7735243	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9292883	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9686159	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9687341	0.81[EUR][1000 genomes]
rs9885467	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881017	chr5:43444826-43731692	Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	222 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10038608	YY2	trans	cerebellum	SCAN
rs10038608	MGC42105	cis	lymphoblastoid	seeQTL
rs10038608	C5orf34	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43433800-43483400	Weak transcription	Gastric	stomach
2	chr5:43440000-43462400	Weak transcription	Colonic Mucosa	Colon
3	chr5:43440800-43466400	Weak transcription	Colon Smooth Muscle	Colon
4	chr5:43440800-43466800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr5:43441600-43466600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr5:43444000-43463600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr5:43444000-43464400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr5:43444000-43467000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr5:43444000-43467000	Weak transcription	Left Ventricle	heart
10	chr5:43444000-43482600	Weak transcription	HMEC	breast
11	chr5:43444200-43467000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:43444200-43472600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr5:43444400-43463800	Weak transcription	Small Intestine	intestine
14	chr5:43444600-43463600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:43444600-43466800	Weak transcription	Brain Angular Gyrus	brain
16	chr5:43444800-43466600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr5:43444800-43482600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr5:43445200-43466800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr5:43448200-43467400	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr5:43448200-43471800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr5:43448400-43466200	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr5:43448800-43463000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr5:43453400-43466200	Weak transcription	Liver	Liver
24	chr5:43453800-43466200	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr5:43453800-43482600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr5:43454000-43482400	Weak transcription	Osteobl	bone
27	chr5:43454800-43466200	Weak transcription	Adipose Nuclei	Adipose
28	chr5:43454800-43482800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr5:43456000-43462800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:43456000-43462800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr5:43457200-43466200	Weak transcription	A549	lung
32	chr5:43457600-43463600	Weak transcription	Esophagus	oesophagus
33	chr5:43459600-43466200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:43459800-43462600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr5:43460000-43462400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr5:43460200-43462400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
37	chr5:43460200-43462400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr5:43460200-43462400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr5:43460400-43462600	Strong transcription	Hela-S3	cervix
40	chr5:43460400-43466200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr5:43460400-43466400	Weak transcription	Primary B cells from peripheral blood	blood
42	chr5:43460400-43467000	Weak transcription	Ovary	ovary
43	chr5:43460400-43467400	Weak transcription	HUVEC	blood vessel
44	chr5:43460400-43472600	Weak transcription	Fetal Kidney	kidney
45	chr5:43460600-43462400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr5:43460600-43466200	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr5:43460600-43471600	Weak transcription	NHDF-Ad	bronchial
48	chr5:43460600-43472000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr5:43460800-43462400	Strong transcription	Primary T cells from cord blood	blood
50	chr5:43460800-43462400	ZNF genes & repeats	Fetal Muscle Leg	muscle

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