Variant report

Variant	rs415590
Chromosome Location	chr6:145851244-145851245
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 147 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs10872579	0.81[CEU][hapmap]
rs110289	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11155438	0.82[CEU][hapmap]
rs12663211	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1292335	0.96[CEU][hapmap];0.95[GIH][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs1292339	0.85[CEU][hapmap]
rs1355146	0.86[EUR][1000 genomes]
rs1396648	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs1883406	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1883407	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1935617	0.86[EUR][1000 genomes]
rs2328704	0.85[CEU][hapmap]
rs365515	0.86[EUR][1000 genomes]
rs365658	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs366621	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs367612	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs367643	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs368848	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs369214	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs372378	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs373313	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs373321	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs373527	0.85[EUR][1000 genomes]
rs373704	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs373778	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs374000	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs374464	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs374728	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs375873	0.92[EUR][1000 genomes]
rs376991	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs377130	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs377143	0.92[EUR][1000 genomes]
rs379164	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs380883	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs382910	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs384453	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs384519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs385134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs386344	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs386678	0.90[EUR][1000 genomes]
rs387965	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs388394	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs388728	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs390252	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs391524	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs391820	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs392014	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs395948	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs396492	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs396681	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs397418	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs399089	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs399516	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs400968	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs401888	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs404229	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs405622	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs406343	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs406799	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs407721	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs408768	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs411468	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs411641	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs413880	0.86[EUR][1000 genomes]
rs413916	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs414222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs414646	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs416243	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs416987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418662	0.92[EUR][1000 genomes]
rs419847	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs419850	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs419854	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs419991	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs421032	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs421268	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs421690	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs425731	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs428659	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs429306	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs430003	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs430248	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs430561	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs434298	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs436066	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs436212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4383831	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs439017	0.86[EUR][1000 genomes]
rs441364	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs441477	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs441575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs442254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs442435	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs444564	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs446242	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs447818	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs449377	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs450076	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs450973	0.91[EUR][1000 genomes]
rs451349	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs452552	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs452770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs453609	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs454370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs454614	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs455109	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4895678	0.86[EUR][1000 genomes]
rs4896831	0.85[CEU][hapmap]
rs4896837	0.81[CEU][hapmap]
rs4896838	0.85[CEU][hapmap]
rs585292	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs636894	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs640544	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6570708	0.82[CEU][hapmap]
rs6901888	0.82[CEU][hapmap]
rs6918814	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6930154	0.81[CEU][hapmap]
rs6941429	0.82[CEU][hapmap]
rs697053	0.82[CEU][hapmap]
rs697054	0.82[CEU][hapmap]
rs697055	0.82[CEU][hapmap]
rs702304	0.82[CEU][hapmap]
rs702307	0.82[CEU][hapmap]
rs702318	0.82[CEU][hapmap]
rs702324	0.82[CEU][hapmap]
rs857881	0.82[CEU][hapmap]
rs9376955	0.88[CEU][hapmap]
rs9390326	0.86[EUR][1000 genomes]
rs9390327	0.84[EUR][1000 genomes]
rs9390329	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9390343	0.84[CEU][hapmap]
rs9390344	0.88[CEU][hapmap]
rs9399549	0.86[EUR][1000 genomes]
rs9399561	0.82[CEU][hapmap]
rs9403706	0.86[EUR][1000 genomes]
rs9403707	0.86[EUR][1000 genomes]
rs9484995	0.85[EUR][1000 genomes]
rs9497316	0.84[EUR][1000 genomes]
rs951143	0.86[EUR][1000 genomes]
rs973855	0.86[EUR][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	nsv886746	chr6:145815949-145920894	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv886747	chr6:145815949-145922777	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1028290	chr6:145819982-145911857	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv886748	chr6:145835917-145911730	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1021041	chr6:145836942-145887333	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1016881	chr6:145840961-145887333	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv538465	chr6:145840961-145887333	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs415590	SHPRH	cis	cerebellum	SCAN
rs415590	SHPRH	cis	parietal	SCAN
rs415590	EPM2A	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145850000-145852600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
2	chr6:145850400-145853200	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr6:145850400-145854200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:145850600-145851400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr6:145850600-145851800	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr6:145850600-145852000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:145850600-145852600	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr6:145850800-145851400	Enhancers	Left Ventricle	heart
9	chr6:145850800-145851400	Enhancers	Pancreas	Pancrea
10	chr6:145850800-145851600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
11	chr6:145850800-145851600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:145850800-145852200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:145850800-145854600	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:145851000-145851600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
15	chr6:145851000-145852400	Enhancers	Stomach Mucosa	stomach
16	chr6:145851000-145853200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
17	chr6:145851200-145851400	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
18	chr6:145851200-145851400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
19	chr6:145851200-145851400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
20	chr6:145851200-145851400	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:145851200-145853000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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