Variant report

Variant	rs7176474
Chromosome Location	chr15:41931506-41931507
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10152332	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10152364	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10775122	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10775123	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10775124	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1081022	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs11070345	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11070347	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11632100	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11634840	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11639146	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11639249	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1197704	0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap]
rs1197772	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[MEX][hapmap]
rs12148330	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12441249	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs12900295	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12902548	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12915325	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12916525	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12916992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16972089	0.93[CEU][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap]
rs1867416	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1867417	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1880937	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1880938	0.83[EUR][1000 genomes]
rs1899819	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1899820	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1899821	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1918314	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[MEX][hapmap]
rs2009310	0.80[ASN][1000 genomes]
rs2141141	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2178004	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2250964	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2577947	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2577950	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2577951	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2577953	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2577954	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2577955	0.83[ASN][1000 genomes]
rs2577958	0.81[EUR][1000 genomes]
rs2577959	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2605570	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs2695162	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2695163	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs2695164	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2695166	0.83[EUR][1000 genomes]
rs2695168	0.81[ASN][1000 genomes]
rs2695169	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2918051	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2925337	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs4244585	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4270151	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4371125	0.90[CHB][hapmap];0.89[ASN][1000 genomes]
rs4465584	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4923908	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4924568	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4924571	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4924572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62002067	0.85[AMR][1000 genomes]
rs62002069	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6493008	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6493010	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7164209	0.89[ASN][1000 genomes]
rs7169496	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7169668	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7177232	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7177911	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7178205	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8027390	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8028886	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8030179	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034261	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8038783	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[MEX][hapmap];0.89[ASN][1000 genomes]
rs8039440	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[MEX][hapmap];0.89[ASN][1000 genomes]

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	nsv1052902	chr15:41869277-41951572	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers 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 lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7176474	TMEM87A	cis	cerebellum	SCAN
rs7176474	ZSCAN29	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41913800-41939400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr15:41914200-41935800	Weak transcription	Gastric	stomach
3	chr15:41924600-41934200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr15:41924800-41937400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr15:41924800-41940400	Weak transcription	Brain Substantia Nigra	brain
6	chr15:41924800-41940400	Weak transcription	Fetal Kidney	kidney
7	chr15:41925000-41935000	Weak transcription	Brain Hippocampus Middle	brain
8	chr15:41925000-41937600	Weak transcription	Pancreas	Pancrea
9	chr15:41925000-41938000	Weak transcription	Colon Smooth Muscle	Colon
10	chr15:41925000-41952200	Weak transcription	Ovary	ovary
11	chr15:41927000-41938800	Weak transcription	A549	lung
12	chr15:41927000-41939400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:41927000-41951800	Weak transcription	Hela-S3	cervix
14	chr15:41927200-41935600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr15:41927200-41939000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr15:41929800-41940400	Weak transcription	Fetal Intestine Small	intestine
17	chr15:41929800-41940800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:41930000-41939400	Weak transcription	HepG2	liver
19	chr15:41931200-41941200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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