Variant report

Variant	rs288172
Chromosome Location	chr5:107353115-107353116
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10035292	0.83[CHB][hapmap]
rs11242662	0.84[CHB][hapmap]
rs149457	0.86[EUR][1000 genomes]
rs15158	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs158172	0.84[ASN][1000 genomes]
rs158173	0.91[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs158175	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs158186	0.88[EUR][1000 genomes]
rs158283	1.00[CEU][hapmap];0.89[TSI][hapmap]
rs158285	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs158415	0.84[CHB][hapmap]
rs158604	0.84[CEU][hapmap]
rs158605	0.84[CEU][hapmap]
rs158606	0.83[CEU][hapmap]
rs158609	0.84[CEU][hapmap];0.80[TSI][hapmap]
rs188274	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs286741	0.91[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]
rs286743	0.91[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]
rs286744	0.91[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]
rs286749	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs286750	0.91[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs286753	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs286771	0.83[CEU][hapmap]
rs286776	0.91[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap]
rs286777	0.90[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap]
rs286779	0.90[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs286781	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs286794	0.84[CHB][hapmap]
rs286802	1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs286809	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs286818	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs288131	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs288139	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs288143	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs288144	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs288145	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs288146	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs288147	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs288149	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs288151	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs288152	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs288154	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs288157	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs288161	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs288164	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs288168	1.00[ASW][hapmap];0.81[GIH][hapmap];0.91[LWK][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs288169	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs288170	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs288171	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs288173	1.00[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs288180	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs288183	1.00[ASW][hapmap];0.89[CHB][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];0.82[TSI][hapmap];0.85[YRI][hapmap]
rs288228	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs288230	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs288232	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs288233	0.83[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs288237	0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs288238	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs289227	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs289228	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs289230	0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34383	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs34388	0.84[CEU][hapmap]
rs34415	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34422	0.83[CEU][hapmap]
rs34423	0.91[CEU][hapmap]
rs34424	0.91[CEU][hapmap]
rs34427	0.91[CEU][hapmap]
rs34428	0.91[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs34432	0.91[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap]
rs365981	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs370216	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs372894	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs40067	0.88[EUR][1000 genomes]
rs40070	0.91[CEU][hapmap]
rs40071	0.91[CEU][hapmap]
rs406139	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41129	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs41131	0.91[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs457378	0.91[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap]
rs4957738	0.83[CHB][hapmap]
rs7728371	0.84[CHB][hapmap]

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	nsv882682	chr5:107213361-107458336	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs288172	SHPK	trans	brain	seeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107319800-107354000	Weak transcription	Primary B cells from cord blood	blood
2	chr5:107327400-107353400	Weak transcription	Aorta	Aorta
3	chr5:107339200-107357400	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr5:107339200-107361200	Weak transcription	Fetal Heart	heart
5	chr5:107339200-107364200	Weak transcription	Left Ventricle	heart
6	chr5:107339600-107364200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:107339600-107373800	Weak transcription	Primary T cells from cord blood	blood
8	chr5:107342600-107355600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr5:107344000-107364200	Weak transcription	Psoas Muscle	Psoas
10	chr5:107344400-107363800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:107347800-107353800	Weak transcription	Spleen	Spleen
12	chr5:107349800-107353400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr5:107350600-107353400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr5:107350800-107356200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:107351400-107355600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:107351600-107354000	Weak transcription	Placenta	Placenta
17	chr5:107352400-107354600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr5:107352400-107354800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr5:107352800-107353400	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr5:107352800-107358200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr5:107352800-107364200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr5:107353000-107353200	Enhancers	Dnd41	blood

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