Variant report

Variant	rs10075281
Chromosome Location	chr5:112060242-112060243
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112058449..112061248-chr5:112063741..112066202,3	K562	blood:
2	chr5:112041541..112044063-chr5:112059728..112062226,2	MCF-7	breast:
3	chr5:112058057..112061004-chr5:112174922..112177064,2	K562	blood:
4	chr5:112053239..112054814-chr5:112058793..112060310,2	K562	blood:
5	chr5:112043098..112044806-chr5:112058262..112061694,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134982	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10051624	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10071425	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10072068	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10075323	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10075377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10076641	0.81[EUR][1000 genomes]
rs10213844	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10463642	0.84[ASN][1000 genomes]
rs10477483	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11241182	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11241183	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11241184	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11241185	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11749701	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12332692	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12513787	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12518091	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12658609	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13156251	0.90[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13173990	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs1441367	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1465910	0.80[EUR][1000 genomes]
rs1530256	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17134858	0.84[CHB][hapmap]
rs17285505	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1866924	0.92[ASW][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1914	0.89[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap]
rs1968557	0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1974786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2019720	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2099810	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2229992	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs2253987	0.81[AMR][1000 genomes]
rs2289484	1.00[ASW][hapmap];0.82[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs2431239	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2431241	0.91[ASW][hapmap];0.89[CEU][hapmap];0.83[GIH][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap]
rs2431512	1.00[ASW][hapmap];0.92[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs2439589	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2439595	0.89[CHB][hapmap]
rs2464803	0.92[ASW][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap]
rs2545156	0.84[ASW][hapmap];0.80[GIH][hapmap];0.83[TSI][hapmap]
rs2546106	0.83[ASW][hapmap];0.85[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap]
rs2546108	0.91[ASW][hapmap];0.89[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes]
rs2546110	1.00[ASW][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2546112	0.84[CHB][hapmap]
rs2546117	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2707763	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2707765	0.89[CEU][hapmap];0.89[CHB][hapmap];0.85[EUR][1000 genomes]
rs28373740	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28578275	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2901844	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2909958	0.82[CEU][hapmap]
rs3317	0.92[ASW][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap]
rs351772	0.82[AMR][1000 genomes]
rs35414976	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs374613	0.84[ASW][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.85[TSI][hapmap]
rs382427	0.82[JPT][hapmap]
rs3846716	0.85[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs390092	0.82[JPT][hapmap]
rs396321	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap]
rs4099181	0.81[CEU][hapmap]
rs414098	0.92[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs419155	0.92[ASW][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap]
rs448162	0.92[ASW][hapmap];0.83[CHD][hapmap]
rs454886	0.84[CHB][hapmap]
rs458906	0.84[EUR][1000 genomes]
rs460137	0.84[ASW][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap]
rs467033	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs4705486	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4705559	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4705573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4705608	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4705610	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4705624	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs518013	0.83[AFR][1000 genomes]
rs548710	0.81[AMR][1000 genomes]
rs6594646	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6862050	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6864688	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs6879057	0.86[EUR][1000 genomes]
rs6894351	0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs6898133	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs7704618	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7727738	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs861674	0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs9326862	0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs9326863	1.00[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs953916	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9647582	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9647583	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][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	nsv830450	chr5:111964170-112134510	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv462387	chr5:112053911-112124369	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv599393	chr5:112053911-112124369	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10075281	MCC	cis	cerebellum	SCAN
rs10075281	TCF7	trans	lymphoblastoid	seeQTL
rs10075281	NCRNA00219	cis	parietal	SCAN
rs10075281	REEP5	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112045400-112062000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr5:112045600-112061600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:112045600-112063600	Weak transcription	Ovary	ovary
4	chr5:112046000-112069200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:112047000-112060400	Weak transcription	Primary B cells from peripheral blood	blood
6	chr5:112047000-112061600	Weak transcription	Aorta	Aorta
7	chr5:112047000-112066000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr5:112047400-112060400	Weak transcription	Fetal Intestine Large	intestine
9	chr5:112047400-112072400	Weak transcription	Thymus	Thymus
10	chr5:112047600-112061600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr5:112048400-112061200	Weak transcription	Fetal Intestine Small	intestine
12	chr5:112049200-112061600	Weak transcription	Fetal Stomach	stomach
13	chr5:112049600-112060400	Weak transcription	Lung	lung
14	chr5:112052000-112072600	Weak transcription	Primary B cells from cord blood	blood
15	chr5:112052600-112072600	Weak transcription	Primary T cells from cord blood	blood
16	chr5:112054400-112060600	Weak transcription	Small Intestine	intestine
17	chr5:112054400-112062200	Weak transcription	Right Ventricle	heart
18	chr5:112054400-112073200	Weak transcription	Pancreas	Pancrea
19	chr5:112054600-112061400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr5:112055000-112061600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr5:112056400-112060800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:112056400-112061800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr5:112056600-112066200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr5:112056600-112067400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr5:112056800-112061800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr5:112056800-112063800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr5:112057400-112060600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr5:112057400-112064800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr5:112058600-112072800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr5:112058800-112064000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr5:112059000-112060800	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr5:112059000-112061000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr5:112059000-112061600	Weak transcription	Psoas Muscle	Psoas
34	chr5:112059200-112067000	Weak transcription	Brain Anterior Caudate	brain
35	chr5:112059200-112067600	Weak transcription	Colon Smooth Muscle	Colon
36	chr5:112059200-112073200	Weak transcription	Left Ventricle	heart
37	chr5:112059600-112060600	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr5:112059800-112060400	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr5:112059800-112060400	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr5:112060000-112061000	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr5:112060000-112072800	Weak transcription	Fetal Heart	heart
42	chr5:112060200-112060600	Enhancers	Brain Hippocampus Middle	brain
43	chr5:112060200-112060800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr5:112060200-112060800	Enhancers	Brain Substantia Nigra	brain
45	chr5:112060200-112061000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr5:112060200-112061000	Enhancers	Skeletal Muscle Male	skeletal muscle

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