Variant report

Variant	rs2008449
Chromosome Location	chr10:38414204-38414205
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 135 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs11011452	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11011461	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1138252	0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1329786	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13503	0.86[CHD][hapmap];0.84[GIH][hapmap]
rs1548255	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs176838	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs176876	0.96[ASN][1000 genomes]
rs176877	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs176879	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs176880	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs176881	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs176882	0.98[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs176885	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs176886	0.87[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs176887	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs176889	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1813028	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1854563	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1985707	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1998062	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2021649	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2021650	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2023299	0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2023351	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2144859	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2178962	0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2180412	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2263162	0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2263163	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2263164	0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2384730	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2384731	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2472150	0.88[CHD][hapmap];0.81[GIH][hapmap]
rs2472173	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2472174	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2472175	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2472176	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2472177	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2472178	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2472179	0.84[ASN][1000 genomes]
rs2472180	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2472181	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2472183	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2474554	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2474563	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2474564	0.93[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2474565	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2474566	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2474567	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2474568	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2474569	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2474570	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.88[MEX][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2474571	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2474572	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2474573	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.83[MKK][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2474574	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2474575	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2474579	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2474580	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2474581	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2474584	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2474586	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2474587	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2474588	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2474590	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2474591	1.00[ASN][1000 genomes]
rs2474594	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2474595	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2474596	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2474597	1.00[ASN][1000 genomes]
rs2474598	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2474599	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2474610	0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2504120	0.98[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2504121	0.96[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2504127	0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2504139	0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2504140	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2504141	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2504142	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2504143	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2504148	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2504149	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2505179	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2505185	0.96[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2505186	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2505187	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2505188	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2505189	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2505190	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2505191	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2505192	0.82[JPT][hapmap]
rs2505193	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2505194	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2505195	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2505196	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2505197	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2505198	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2505202	0.94[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];1.00[YRI][hapmap]
rs2505203	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2505235	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2505236	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2505237	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2505241	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2505244	0.99[ASN][1000 genomes]
rs2505248	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2505249	0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2505250	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2505251	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2505252	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2505258	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2505259	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2505260	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2800485	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap]
rs2983343	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs496627	0.86[CHD][hapmap];0.84[GIH][hapmap]
rs626519	0.86[CHD][hapmap];0.84[GIH][hapmap]
rs645064	0.88[CHD][hapmap];0.84[GIH][hapmap]
rs6482060	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs71491246	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7915062	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9299760	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs932538	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9418322	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895030	chr10:37715737-38674609	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1045684	chr10:37765361-38426204	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv540564	chr10:37765361-38426204	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1040704	chr10:37940024-38451917	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv1051121	chr10:38155991-38426204	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv540565	chr10:38155991-38426204	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv540566	chr10:38301001-38680127	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv550419	chr10:38311777-38501654	Enhancers Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv6465	chr10:38377662-38422125	Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv895031	chr10:38402789-38464886	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2008449	HSD17B7P2	cis	Whole Blood	GTEx
rs2008449	ZNF37A	cis	lymphoblastoid	seeQTL
rs2008449	ZNF37A	cis	parietal	SCAN
rs2008449	ZNF25	cis	cerebellum	SCAN
rs2008449	HSD17B7P2	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38400600-38416600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
2	chr10:38400800-38415000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr10:38411200-38414600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr10:38413400-38414600	Weak transcription	Brain Germinal Matrix	brain
5	chr10:38413400-38420400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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