Variant report

Variant	rs10162627
Chromosome Location	chr15:74299870-74299871
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:74284526..74286693-chr15:74299037..74301704,2	MCF-7	breast:
2	chr15:74289396..74290975-chr15:74298748..74301175,2	K562	blood:
3	chr15:74299747..74301420-chr15:74301647..74303236,2	MCF-7	breast:
4	chr15:74283960..74290618-chr15:74296413..74304371,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140464	Chromatin interaction
ENSG00000067221	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1052242	0.96[CEU][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes]
rs1052246	0.95[CEU][hapmap];0.85[AMR][1000 genomes]
rs1078555	0.80[YRI][hapmap]
rs10851868	0.94[ASW][hapmap];0.96[CEU][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes]
rs11072458	0.86[CEU][hapmap]
rs11072462	0.82[CEU][hapmap]
rs11072463	0.81[CEU][hapmap];0.95[MEX][hapmap]
rs11072464	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11072465	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11072466	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11072467	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11072469	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11633520	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11636016	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636065	0.96[CEU][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes]
rs11636150	0.83[AMR][1000 genomes]
rs11854321	0.81[AMR][1000 genomes]
rs12442211	0.83[MEX][hapmap]
rs12592370	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12593528	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12901603	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902857	0.96[CEU][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes]
rs12904213	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12908748	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12912395	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12917179	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1550434	0.88[YRI][hapmap]
rs2277599	0.96[CEU][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes]
rs2304715	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304716	0.82[CEU][hapmap];0.83[MEX][hapmap]
rs2304717	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2304718	0.83[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3784561	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3784562	1.00[CEU][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs4287518	0.82[CEU][hapmap]
rs4886820	0.80[AMR][1000 genomes]
rs4886844	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4886845	0.83[AMR][1000 genomes]
rs4886846	0.82[AMR][1000 genomes]
rs734854	0.95[MEX][hapmap]
rs743581	0.80[ASN][1000 genomes]
rs8027327	0.96[CEU][hapmap];0.85[AMR][1000 genomes]
rs8027447	0.96[CEU][hapmap];0.83[AMR][1000 genomes]
rs8027774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8028557	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8039276	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8043489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758387	chr15:74215114-74464916	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv2760040	chr15:74215114-74464916	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv428308	chr15:74215114-74464916	Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv833052	chr15:74250378-74377150	Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv518316	chr15:74290993-74331083	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv469619	chr15:74291859-74466321	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv482362	chr15:74291859-74466321	Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10162627	KIAA1462	trans	parietal	SCAN
rs10162627	LARP6	cis	parietal	SCAN
rs10162627	CYP11A1	cis	cerebellum	SCAN
rs10162627	STOML1	cis	cerebellum	SCAN
rs10162627	BBS4	cis	parietal	SCAN
rs10162627	ADPGK	cis	parietal	SCAN
rs10162627	PML	cis	multi-tissue	Pritchard
rs10162627	STOML1	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74288200-74301800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr15:74288200-74303000	Weak transcription	A549	lung
3	chr15:74288200-74303800	Weak transcription	Brain Angular Gyrus	brain
4	chr15:74288200-74331000	Weak transcription	Fetal Heart	heart
5	chr15:74289600-74302400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr15:74289800-74303200	Weak transcription	Brain Substantia Nigra	brain
7	chr15:74289800-74331000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr15:74290000-74303400	Weak transcription	Fetal Kidney	kidney
9	chr15:74290000-74314800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr15:74290800-74301600	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr15:74291000-74300000	Weak transcription	Aorta	Aorta
12	chr15:74291000-74311200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr15:74291000-74314800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:74291000-74315000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr15:74291000-74315200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr15:74291400-74300000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr15:74291600-74300200	Weak transcription	Brain Anterior Caudate	brain
18	chr15:74291800-74314800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:74292000-74300200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr15:74292000-74300800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr15:74292000-74302400	Strong transcription	Osteobl	bone
22	chr15:74292000-74315200	Weak transcription	Fetal Brain Female	brain
23	chr15:74292000-74329200	Weak transcription	Fetal Brain Male	brain
24	chr15:74293400-74303600	Weak transcription	NH-A	brain
25	chr15:74294000-74300800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr15:74294400-74300000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr15:74294600-74300400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr15:74294800-74300200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr15:74295600-74300000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr15:74296000-74300000	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr15:74296400-74301400	Weak transcription	NHDF-Ad	bronchial
32	chr15:74296600-74315200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr15:74296800-74300200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr15:74296800-74315200	Weak transcription	Brain Germinal Matrix	brain
35	chr15:74297000-74302000	Weak transcription	Ovary	ovary
36	chr15:74297000-74315200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr15:74297000-74315600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr15:74297400-74300400	Strong transcription	HSMMtube	muscle
39	chr15:74297600-74301400	Strong transcription	Hela-S3	cervix
40	chr15:74297800-74300800	Genic enhancers	Duodenum Smooth Muscle	Duodenum
41	chr15:74297800-74300800	Genic enhancers	Placenta	Placenta
42	chr15:74297800-74300800	Genic enhancers	Thymus	Thymus
43	chr15:74297800-74301400	Strong transcription	NHEK	skin
44	chr15:74297800-74301800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr15:74298000-74300400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr15:74298000-74300600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:74298000-74300600	Genic enhancers	Lung	lung
48	chr15:74298000-74300600	Strong transcription	Dnd41	blood
49	chr15:74298000-74300600	Strong transcription	K562	blood
50	chr15:74298000-74300600	Strong transcription	NHLF	lung

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