Variant report

Variant	rs17680671
Chromosome Location	chr19:21576563-21576564
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 29 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs11085441	0.86[CEU][hapmap]
rs11085447	0.84[CEU][hapmap]
rs11667770	0.89[CEU][hapmap]
rs11671832	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12975081	0.84[CEU][hapmap]
rs12975981	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs12981564	0.89[CEU][hapmap]
rs12981735	0.89[CEU][hapmap]
rs12981869	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs12982282	0.89[CEU][hapmap]
rs12984871	0.81[EUR][1000 genomes]
rs1678822	0.85[CHB][hapmap]
rs17618715	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs17618778	0.82[CHB][hapmap]
rs1762580	0.89[ASN][1000 genomes]
rs1781873	0.89[CEU][hapmap]
rs1827225	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2012013	0.89[CEU][hapmap]
rs2086320	0.82[EUR][1000 genomes]
rs2088762	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs2102072	0.82[EUR][1000 genomes]
rs2127407	0.81[EUR][1000 genomes]
rs2127408	0.81[EUR][1000 genomes]
rs2170024	0.90[CEU][hapmap];0.91[YRI][hapmap]
rs2170025	0.81[EUR][1000 genomes]
rs2358991	0.81[EUR][1000 genomes]
rs2358992	0.81[EUR][1000 genomes]
rs2434997	0.81[EUR][1000 genomes]
rs2914636	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs2914637	0.89[ASN][1000 genomes]
rs2914638	0.89[CEU][hapmap];0.89[YRI][hapmap]
rs2914648	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2914649	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2928210	0.89[ASN][1000 genomes]
rs2937158	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2937159	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2968084	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34875588	0.89[ASN][1000 genomes]
rs35860067	0.89[ASN][1000 genomes]
rs4315457	0.89[CEU][hapmap]
rs4621113	0.89[CEU][hapmap]
rs483383	0.89[ASN][1000 genomes]
rs488125	0.89[YRI][hapmap]
rs501647	1.00[CHB][hapmap];0.90[YRI][hapmap];0.89[ASN][1000 genomes]
rs504280	0.80[YRI][hapmap]
rs509540	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs514390	0.84[ASN][1000 genomes]
rs549882	0.89[ASN][1000 genomes]
rs552039	0.89[ASN][1000 genomes]
rs566230	1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs57055133	0.89[ASN][1000 genomes]
rs58121117	0.89[ASN][1000 genomes]
rs59617671	0.89[ASN][1000 genomes]
rs608002	0.89[ASN][1000 genomes]
rs62107470	0.89[ASN][1000 genomes]
rs62107538	0.89[ASN][1000 genomes]
rs62109224	0.89[ASN][1000 genomes]
rs62110379	0.89[ASN][1000 genomes]
rs62110417	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62110418	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs629548	0.82[CHB][hapmap]
rs635730	0.82[ASN][1000 genomes]
rs6511239	0.96[CEU][hapmap]
rs669046	0.85[CHB][hapmap]
rs670813	0.89[ASN][1000 genomes]
rs685844	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs7245848	0.89[ASN][1000 genomes]
rs7246684	0.89[ASN][1000 genomes]
rs7247411	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs7248601	0.83[CEU][hapmap]
rs7248700	0.87[ASN][1000 genomes]
rs7249412	0.90[CEU][hapmap]
rs7252261	0.89[CEU][hapmap]
rs7254436	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7254762	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7257857	0.89[CEU][hapmap]
rs7259311	0.90[CEU][hapmap]
rs73025767	0.89[ASN][1000 genomes]
rs7508671	0.95[CEU][hapmap]
rs8099863	0.89[ASN][1000 genomes]
rs8099940	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs8103325	0.89[CEU][hapmap]
rs8103411	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8103417	0.84[ASN][1000 genomes]
rs8103459	0.92[CEU][hapmap]
rs8105404	0.89[ASN][1000 genomes]
rs8105629	0.82[CHB][hapmap];0.83[YRI][hapmap]
rs8107999	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8110967	0.90[CEU][hapmap]
rs8111189	1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs8112583	0.81[EUR][1000 genomes]
rs8113558	0.82[CHB][hapmap]
rs924487	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription 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	41 gene(s)	inside rSNPs	diseases
3	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv911420	chr19:21454672-21613397	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers 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	31 gene(s)	inside rSNPs	diseases
8	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	esv1793996	chr19:21544242-21609607	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv1801985	chr19:21544242-21609607	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	esv1844586	chr19:21544242-21609607	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	esv1834499	chr19:21557835-21609607	Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	esv1834993	chr19:21557835-21609607	Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:29)

SNP	Gene	Cis/trans	Tissue	Source
rs17680671	RP11-678G14.2	cis	Skin Sun Exposed Lower leg	GTEx
rs17680671	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs17680671	CTD-2561J22.5	cis	Esophagus Muscularis	GTEx
rs17680671	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs17680671	LOC115648	cis	normal skin	skin_eQTL
rs17680671	RP11-678G14.2	cis	Whole Blood	GTEx
rs17680671	CTD-2561J22.5	cis	Thyroid	GTEx
rs17680671	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs17680671	ZNF429	cis	Whole Blood	GTEx
rs17680671	CTD-2561J22.5	cis	Nerve Tibial	GTEx
rs17680671	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs17680671	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs17680671	RP11-678G14.2	cis	Nerve Tibial	GTEx
rs17680671	ZNF493	cis	Lymphoblastoid	GTEx
rs17680671	CTD-2561J22.5	cis	lung	GTEx
rs17680671	RP11-678G14.3	cis	lung	GTEx
rs17680671	RP11-678G14.2	cis	Thyroid	GTEx
rs17680671	RP11-420K14.2	cis	Heart Left Ventricle	GTEx
rs17680671	RP11-678G14.2	cis	Artery Tibial	GTEx
rs17680671	RP11-678G14.2	cis	lung	GTEx
rs17680671	ZNF493	cis	multi-tissue	Pritchard
rs17680671	CTD-2561J22.5	cis	Skin Sun Exposed Lower leg	GTEx
rs17680671	CTD-2561J22.5	cis	Stomach	GTEx
rs17680671	RP11-678G14.3	cis	Muscle Skeletal	GTEx
rs17680671	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs17680671	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs17680671	LOC115648	cis	uninvolved skin	skin_eQTL
rs17680671	RP11-678G14.2	cis	Muscle Skeletal	GTEx
rs17680671	ZNF493	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21567400-21579800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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