Variant report

Variant	rs28557159
Chromosome Location	chr15:41657353-41657354
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 141 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs10518717	0.93[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851403	1.00[ASN][1000 genomes]
rs11070328	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11629979	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630656	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs11630799	1.00[ASN][1000 genomes]
rs11631770	0.83[ASW][hapmap]
rs11633799	0.90[GIH][hapmap];0.84[MEX][hapmap]
rs11635269	1.00[ASN][1000 genomes]
rs11635565	1.00[ASN][1000 genomes]
rs11635906	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11854081	0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854632	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs11854820	1.00[ASN][1000 genomes]
rs11858068	1.00[ASN][1000 genomes]
rs11858812	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs13313520	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329235	1.00[ASN][1000 genomes]
rs13329579	1.00[ASN][1000 genomes]
rs13379756	0.90[GIH][hapmap]
rs16971726	1.00[CHB][hapmap]
rs16971767	0.97[GIH][hapmap];0.84[MEX][hapmap]
rs16971798	0.81[GIH][hapmap]
rs1757468	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17730589	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs17730888	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866399	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1899	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs2118740	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2448402	1.00[ASN][1000 genomes]
rs2730056	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs2730058	1.00[ASN][1000 genomes]
rs2777491	0.88[ASW][hapmap];0.81[GIH][hapmap];0.82[YRI][hapmap]
rs28374715	1.00[CHB][hapmap]
rs28377562	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382348	1.00[ASN][1000 genomes]
rs28416360	1.00[ASN][1000 genomes]
rs28421136	1.00[ASN][1000 genomes]
rs28437576	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28448670	0.81[EUR][1000 genomes]
rs28456082	1.00[ASN][1000 genomes]
rs28458941	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28463309	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28477406	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28492932	1.00[ASN][1000 genomes]
rs28493087	1.00[ASN][1000 genomes]
rs28493702	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs28526381	0.97[GIH][hapmap];0.84[MEX][hapmap]
rs28535540	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28554139	1.00[CHB][hapmap]
rs28555198	1.00[ASN][1000 genomes]
rs28576457	1.00[ASN][1000 genomes]
rs28584379	1.00[ASN][1000 genomes]
rs28617619	1.00[ASN][1000 genomes]
rs28623183	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28631111	1.00[CHB][hapmap]
rs28661013	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28663426	1.00[ASN][1000 genomes]
rs28673484	1.00[ASN][1000 genomes]
rs28687846	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28700583	1.00[ASN][1000 genomes]
rs28703570	1.00[ASN][1000 genomes]
rs28712264	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28716689	1.00[ASN][1000 genomes]
rs28827035	1.00[ASN][1000 genomes]
rs28897479	1.00[ASN][1000 genomes]
rs316604	0.87[CEU][hapmap];1.00[ASN][1000 genomes]
rs316605	0.94[ASW][hapmap];0.81[GIH][hapmap];0.82[YRI][hapmap]
rs316606	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs316607	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs316609	0.86[YRI][hapmap]
rs316610	0.94[ASW][hapmap];0.81[GIH][hapmap];0.82[YRI][hapmap]
rs316611	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs316614	0.88[ASW][hapmap];0.81[GIH][hapmap];0.82[YRI][hapmap]
rs316616	1.00[ASN][1000 genomes]
rs3204853	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs34040639	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs34665396	1.00[ASN][1000 genomes]
rs3743038	1.00[ASW][hapmap];0.90[GIH][hapmap];0.84[MEX][hapmap];0.93[YRI][hapmap]
rs4924549	1.00[CHB][hapmap]
rs513280	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs521890	1.00[ASN][1000 genomes]
rs522063	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs55725658	1.00[ASN][1000 genomes]
rs56341337	0.81[EUR][1000 genomes]
rs56400990	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59000092	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493000	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493003	1.00[ASN][1000 genomes]
rs691011	1.00[ASN][1000 genomes]
rs691906	1.00[ASN][1000 genomes]
rs691907	1.00[ASN][1000 genomes]
rs7162231	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163788	1.00[ASW][hapmap];0.82[YRI][hapmap]
rs7163989	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164211	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs7164684	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs7165396	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165914	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167706	1.00[ASN][1000 genomes]
rs7168002	1.00[ASN][1000 genomes]
rs7168307	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168431	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs7169543	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7176588	0.83[GIH][hapmap];0.84[MEX][hapmap]
rs7177641	0.94[ASW][hapmap];0.82[YRI][hapmap]
rs7178634	0.97[GIH][hapmap];0.84[MEX][hapmap]
rs7178777	0.97[GIH][hapmap];0.84[MEX][hapmap]
rs7180418	0.97[GIH][hapmap];0.84[MEX][hapmap]
rs7181982	0.93[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182324	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72737786	1.00[ASN][1000 genomes]
rs72737792	1.00[ASN][1000 genomes]
rs72737793	1.00[ASN][1000 genomes]
rs72739630	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72739644	1.00[ASN][1000 genomes]
rs8023530	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026197	0.86[YRI][hapmap]
rs8030228	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8032838	0.97[GIH][hapmap];0.84[MEX][hapmap]
rs8034840	1.00[ASN][1000 genomes]
rs8036026	0.93[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036498	0.94[GIH][hapmap];0.84[MEX][hapmap]
rs8036734	1.00[ASN][1000 genomes]
rs8037574	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038132	1.00[ASN][1000 genomes]
rs8038983	1.00[ASN][1000 genomes]
rs8041325	0.88[ASW][hapmap];0.81[GIH][hapmap]
rs8041809	1.00[ASN][1000 genomes]
rs8043237	1.00[ASN][1000 genomes]
rs823716	0.82[YRI][hapmap]
rs919961	0.97[GIH][hapmap];0.84[MEX][hapmap]
rs9302109	0.97[GIH][hapmap];0.84[MEX][hapmap]
rs9568	0.94[CEU][hapmap];1.00[CHB][hapmap];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	nsv1044438	chr15:41560160-41745480	Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv1038923	chr15:41585028-41754890	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv1045142	chr15:41585044-41738314	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv1039283	chr15:41620499-41745480	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
5	nsv933757	chr15:41641236-41773058	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases
6	esv3443258	chr15:41644871-41681515	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3409890	chr15:41644895-41681538	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs28557159	SPINT1	cis	cerebellum	SCAN
rs28557159	NDUFAF1	cis	parietal	SCAN
rs28557159	NDUFAF1	cis	cerebellum	SCAN
rs28557159	RASGRP1	cis	cerebellum	SCAN
rs28557159	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs28557159	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs28557159	OIP5-AS1	cis	Artery Tibial	GTEx
rs28557159	OIP5-AS1	cis	Nerve Tibial	GTEx
rs28557159	OIP5-AS1	cis	Esophagus Mucosa	GTEx
rs28557159	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs28557159	NUSAP1	cis	cerebellum	SCAN
rs28557159	NDUFAF1	cis	multi-tissue	Pritchard
rs28557159	GPR176	cis	parietal	SCAN
rs28557159	NDUFAF1	cis	lung	GTEx
rs28557159	NUSAP1	cis	parietal	SCAN
rs28557159	NDUFAF1	cis	Thyroid	GTEx
rs28557159	NDUFAF1	cis	lymphoblastoid	seeQTL
rs28557159	NDUFAF1	cis	Muscle Skeletal	GTEx
rs28557159	OIP5-AS1	cis	Esophagus Muscularis	GTEx
rs28557159	RPAP1	cis	parietal	SCAN
rs28557159	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs28557159	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs28557159	OIP5-AS1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41625400-41670200	Weak transcription	Gastric	stomach
2	chr15:41625600-41659200	Weak transcription	Lung	lung
3	chr15:41625800-41665800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:41625800-41694200	Weak transcription	Small Intestine	intestine
5	chr15:41626000-41665200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:41626200-41658200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr15:41626200-41678200	Weak transcription	Liver	Liver
8	chr15:41626200-41680200	Weak transcription	Fetal Brain Male	brain
9	chr15:41626400-41677800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:41626400-41678400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr15:41626800-41686400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr15:41627000-41672800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:41627200-41676800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr15:41627400-41668000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr15:41627400-41673000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:41628200-41673000	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:41628600-41672800	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr15:41628600-41673800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:41629000-41672000	Weak transcription	Primary T cells from cord blood	blood
20	chr15:41629000-41673000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:41629400-41672400	Strong transcription	Fetal Stomach	stomach
22	chr15:41629400-41672800	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr15:41629400-41673600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr15:41629600-41674000	Strong transcription	Fetal Thymus	thymus
25	chr15:41629800-41658800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr15:41630000-41662000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr15:41630400-41674000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr15:41630400-41674200	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr15:41630800-41673800	Strong transcription	Dnd41	blood
30	chr15:41631200-41659200	Weak transcription	Primary B cells from peripheral blood	blood
31	chr15:41631800-41679200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr15:41632000-41673000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr15:41632000-41673600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr15:41632200-41659600	Strong transcription	Fetal Muscle Leg	muscle
35	chr15:41632200-41674000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr15:41632800-41673800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr15:41638400-41658800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr15:41639200-41671800	Strong transcription	Hela-S3	cervix
39	chr15:41639800-41657400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr15:41640800-41674000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr15:41642800-41679400	Weak transcription	Ovary	ovary
42	chr15:41643600-41658800	Weak transcription	Fetal Brain Female	brain
43	chr15:41643800-41658800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr15:41643800-41659000	Weak transcription	Fetal Heart	heart
45	chr15:41643800-41679000	Weak transcription	Pancreas	Pancrea
46	chr15:41644000-41658600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:41644000-41659200	Weak transcription	Spleen	Spleen
48	chr15:41644000-41670200	Weak transcription	Placenta	Placenta
49	chr15:41644200-41678600	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr15:41644200-41679800	Weak transcription	Primary B cells from cord blood	blood

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