Variant report

Variant	rs10908465
Chromosome Location	chr1:155389688-155389689
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:155383989..155385570-chr1:155389666..155391929,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238805	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10752611	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10796943	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10796944	0.87[AMR][1000 genomes]
rs10796945	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10796946	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10796947	0.91[ASN][1000 genomes]
rs10908463	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap]
rs10908466	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10908467	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10908469	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10908470	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10908471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10908472	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11264359	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs11264361	0.88[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs11264363	0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs11264366	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11264367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11264369	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11264370	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11264371	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264372	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264374	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11264375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11264380	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11264381	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11264383	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11264386	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11264387	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap]
rs11582072	0.91[ASN][1000 genomes]
rs12024696	0.80[EUR][1000 genomes]
rs12025532	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12026638	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12028416	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12030596	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12037824	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12041534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12046473	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12067371	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12079134	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12081067	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12143948	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs12239100	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12239114	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12724079	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12746592	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1325908	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1360554	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.90[ASN][1000 genomes]
rs1556488	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs1886905	0.96[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs2025669	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2297480	0.88[CEU][hapmap];0.89[CHB][hapmap];0.82[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs35615695	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.85[ASN][1000 genomes]
rs3892792	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs5005770	1.00[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];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56675301	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6670014	0.83[AMR][1000 genomes]
rs6684889	0.89[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs6688636	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.91[ASN][1000 genomes]
rs66923802	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6696888	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.87[ASN][1000 genomes]
rs71517782	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7411786	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7416976	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7556102	0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	nsv831636	chr1:155219223-155444864	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
4	esv1799856	chr1:155305059-155534616	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	esv1795662	chr1:155305059-155540660	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	esv1795478	chr1:155334933-155510824	Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv1803551	chr1:155334933-155522572	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	esv1800974	chr1:155367680-155510824	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10908465	YY1AP1	cis	parietal	SCAN
rs10908465	SPRR2D	cis	parietal	SCAN
rs10908465	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs10908465	GBA	cis	Esophagus Mucosa	GTEx
rs10908465	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs10908465	SPRR2A	cis	cerebellum	SCAN
rs10908465	YY1AP1	cis	cerebellum	SCAN
rs10908465	GBAP1	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155312400-155407400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:155345600-155403000	Weak transcription	Esophagus	oesophagus
3	chr1:155347400-155407400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:155349400-155407600	Weak transcription	Aorta	Aorta
5	chr1:155349800-155390800	Weak transcription	Brain Anterior Caudate	brain
6	chr1:155349800-155403000	Weak transcription	NHLF	lung
7	chr1:155350000-155399200	Weak transcription	Brain Angular Gyrus	brain
8	chr1:155350000-155402400	Weak transcription	Brain Substantia Nigra	brain
9	chr1:155350200-155399200	Weak transcription	NH-A	brain
10	chr1:155357200-155400600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:155358200-155398400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:155358600-155397000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:155359400-155407200	Weak transcription	Pancreas	Pancrea
14	chr1:155361400-155406800	Weak transcription	Fetal Heart	heart
15	chr1:155362200-155433400	Weak transcription	Psoas Muscle	Psoas
16	chr1:155362800-155442400	Weak transcription	Right Ventricle	heart
17	chr1:155363000-155407400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:155364400-155450800	Weak transcription	HUVEC	blood vessel
19	chr1:155365000-155399000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:155365000-155407800	Weak transcription	Fetal Kidney	kidney
21	chr1:155365200-155390800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:155365200-155403000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:155365200-155406800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:155365200-155407000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr1:155365400-155396400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:155365400-155402600	Weak transcription	Small Intestine	intestine
27	chr1:155365400-155406600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr1:155365600-155404800	Weak transcription	NHDF-Ad	bronchial
29	chr1:155365600-155406800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:155365600-155407200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:155367400-155426000	Weak transcription	Stomach Mucosa	stomach
32	chr1:155374800-155390600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr1:155374800-155394600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:155375600-155390600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:155375800-155397600	Weak transcription	Lung	lung
36	chr1:155376400-155400600	Weak transcription	Spleen	Spleen
37	chr1:155378200-155399000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:155378800-155399000	Weak transcription	Primary B cells from cord blood	blood
39	chr1:155380800-155393400	Weak transcription	HSMMtube	muscle
40	chr1:155381000-155399200	Weak transcription	Left Ventricle	heart
41	chr1:155381200-155393800	Weak transcription	Primary hematopoietic stem cells	blood
42	chr1:155381600-155392800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:155381800-155398800	Weak transcription	Fetal Lung	lung
44	chr1:155381800-155407200	Weak transcription	HMEC	breast
45	chr1:155382000-155399000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:155382600-155393800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:155382600-155394000	Weak transcription	Fetal Muscle Trunk	muscle
48	chr1:155382600-155400600	Weak transcription	Colonic Mucosa	Colon
49	chr1:155382600-155406600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr1:155382600-155408000	Weak transcription	Ovary	ovary

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