Variant report

Variant	rs4985942
Chromosome Location	chr17:20864536-20864537
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr17:20864520-20864670	NHEK	skin:	n/a	n/a
2	TCF7L2	chr17:20864240-20864731	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
ENSG00000264660	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10153263	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10512422	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11541314	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11650653	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11869201	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11869217	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11869959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12450389	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12452171	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12937950	1.00[ASN][1000 genomes]
rs12947514	0.82[ASN][1000 genomes]
rs16962364	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1871275	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2127096	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2364323	1.00[CHB][hapmap]
rs28663143	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2886049	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs34354508	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35022634	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4381653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4427861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4985945	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57522885	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6587107	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587113	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6587116	1.00[ASN][1000 genomes]
rs66487709	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66516868	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs719094	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73303698	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8072149	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8080321	0.86[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs984007	0.95[CEU][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9893047	0.82[ASN][1000 genomes]
rs9895277	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9895618	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9896853	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9907786	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9909279	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9914758	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9914916	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751619	chr17:20462908-20914156	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv1064365	chr17:20801739-20890716	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv949097	chr17:20801739-21406355	Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv574597	chr17:20802778-20872331	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv527161	chr17:20814766-20872331	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv457706	chr17:20814766-20872331	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv574598	chr17:20814766-20872331	Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv529759	chr17:20839079-21529632	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
9	nsv2006	chr17:20846763-20892730	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4985942	RP11-381P6.1	cis	Muscle Skeletal	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20835600-20869000	Weak transcription	HepG2	liver
2	chr17:20847800-20869400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:20848200-20864600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr17:20848200-20872200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr17:20848200-20896600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr17:20848400-20865000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr17:20852800-20882600	Weak transcription	K562	blood
8	chr17:20857800-20867600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:20859000-20881800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr17:20859200-20867000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr17:20859600-20864800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr17:20862600-20890800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr17:20862800-20864800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr17:20862800-20866200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr17:20864000-20864600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr17:20864000-20865000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr17:20864000-20865800	Enhancers	H1 Cell Line	embryonic stem cell
18	chr17:20864200-20865800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr17:20864200-20866000	Enhancers	HMEC	breast
20	chr17:20864200-20866600	Enhancers	Placenta	Placenta
21	chr17:20864400-20864600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr17:20864400-20865000	Flanking Active TSS	NHEK	skin
23	chr17:20864400-20865400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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