Variant report

Variant	rs11854667
Chromosome Location	chr15:49640313-49640314
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:49635452..49638613-chr15:49638913..49642662,3	K562	blood:
2	chr15:49639583..49641863-chr15:49642641..49645261,2	K562	blood:

Extended variants
information (count: 109 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10467992	0.90[JPT][hapmap]
rs10467993	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10851475	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10851476	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11070685	0.80[YRI][hapmap]
rs11070687	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070692	0.85[JPT][hapmap]
rs11852825	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12437486	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12438777	0.80[AMR][1000 genomes]
rs12899761	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12902497	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12903238	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12903904	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12904171	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12909779	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916840	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1429556	0.84[JPT][hapmap]
rs1594188	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16962111	0.80[AMR][1000 genomes]
rs1816293	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864299	0.89[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1904313	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1904314	0.93[ASN][1000 genomes]
rs1981995	0.89[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2043036	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2099141	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2163095	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163096	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247517	0.92[CEU][hapmap];0.84[CHB][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2263559	0.80[AMR][1000 genomes]
rs2264508	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2413935	0.85[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs2413941	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2439133	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2457228	0.85[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs2457229	0.80[EUR][1000 genomes]
rs2663089	0.85[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs28374976	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28653543	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28687437	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2899431	0.96[CEU][hapmap];0.83[CHB][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2940746	0.80[AMR][1000 genomes]
rs3098613	0.89[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.80[EUR][1000 genomes]
rs3098619	0.89[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3098621	0.96[CEU][hapmap];0.84[CHB][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3105858	0.96[CEU][hapmap];0.84[CHB][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3105864	0.89[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.80[EUR][1000 genomes]
rs3105866	0.80[AMR][1000 genomes]
rs3907313	1.00[CEU][hapmap];0.84[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4316697	0.80[JPT][hapmap]
rs4393519	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4421927	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4508377	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774537	0.96[CEU][hapmap];0.84[CHB][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4775810	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs481466	0.89[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs489813	0.80[AMR][1000 genomes]
rs520495	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs568726	0.85[CEU][hapmap]
rs577614	0.82[YRI][hapmap]
rs604765	0.96[CEU][hapmap];0.84[CHB][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs609434	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs612803	0.96[CEU][hapmap];0.84[CHB][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs619045	0.80[AMR][1000 genomes]
rs62009779	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs626295	0.89[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs626855	0.85[CEU][hapmap]
rs633333	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6493356	0.96[CEU][hapmap];0.84[CHB][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6493357	0.96[CEU][hapmap];0.83[CHB][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6493359	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6493362	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493363	0.81[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs6493366	0.83[YRI][hapmap]
rs6493367	0.83[YRI][hapmap]
rs66499252	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs672777	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs685172	0.85[CEU][hapmap]
rs694882	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7162360	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7166847	0.96[CEU][hapmap];0.84[CHB][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7168201	0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7169443	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7173761	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7177959	0.80[YRI][hapmap]
rs7179127	0.89[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7179237	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs735495	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8024102	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025237	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8031480	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.80[JPT][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8034112	0.97[AFR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8034747	0.90[JPT][hapmap]
rs8034956	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8035266	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8039512	0.96[CEU][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8039920	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040116	0.80[YRI][hapmap]
rs8040134	0.89[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[GIH][hapmap];0.80[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8041461	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8182081	0.81[EUR][1000 genomes]
rs919447	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9806208	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9806776	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs981612	0.94[ASW][hapmap];0.83[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039220	chr15:49492509-49644261	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv833002	chr15:49621400-49781799	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11854667	SPATA5L1	cis	parietal	SCAN
rs11854667	LCMT2	cis	parietal	SCAN
rs11854667	COPS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49613600-49643000	Weak transcription	Pancreas	Pancrea
2	chr15:49616000-49641400	Weak transcription	Fetal Lung	lung
3	chr15:49622600-49642600	Weak transcription	HSMM	muscle
4	chr15:49623200-49646000	Weak transcription	Left Ventricle	heart
5	chr15:49623400-49647600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:49628600-49640800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr15:49632400-49643000	Weak transcription	Lung	lung
8	chr15:49636000-49640400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr15:49636000-49640600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr15:49636200-49640400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr15:49636200-49645200	Weak transcription	HUVEC	blood vessel
12	chr15:49637000-49640600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr15:49637000-49640600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr15:49637600-49644000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr15:49638800-49641000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:49638800-49642600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr15:49638800-49643000	Weak transcription	Aorta	Aorta

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