Variant report

Variant	rs3851786
Chromosome Location	chr17:45046932-45046933
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	POLR2A	chr17:45046702-45046954	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr17:45046606-45046975	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:45046598..45049748-chr17:45053753..45056442,3	MCF-7	breast:

Variant related genes	Relation type
MIR5089	TF binding region
ENSG00000263142	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1047779	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1052504	0.94[ASN][1000 genomes]
rs1052586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10853085	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10853087	0.94[ASN][1000 genomes]
rs11079742	0.88[CEU][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs11079745	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11079750	0.83[CEU][hapmap]
rs11652318	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11654971	0.94[ASN][1000 genomes]
rs11655668	0.87[JPT][hapmap]
rs11656362	0.95[ASN][1000 genomes]
rs11658276	0.92[ASN][1000 genomes]
rs11869840	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12601886	0.94[ASN][1000 genomes]
rs12940071	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1618989	0.93[ASN][1000 genomes]
rs1623402	0.94[ASN][1000 genomes]
rs1662576	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1662577	0.94[ASN][1000 genomes]
rs1662594	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1662596	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1662597	0.92[ASN][1000 genomes]
rs17608961	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1838105	0.82[JPT][hapmap]
rs1867237	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs189899	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs197912	0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs197913	0.83[ASN][1000 genomes]
rs197915	0.85[ASN][1000 genomes]
rs197917	0.92[ASN][1000 genomes]
rs197918	0.94[ASN][1000 genomes]
rs197919	0.94[ASN][1000 genomes]
rs197922	0.82[JPT][hapmap]
rs197923	0.83[JPT][hapmap]
rs197925	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs197926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2003538	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2003539	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2072317	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs2191033	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2316330	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2317997	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28553405	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2920396	0.94[ASN][1000 genomes]
rs2920397	0.94[ASN][1000 genomes]
rs35707546	0.92[ASN][1000 genomes]
rs3760377	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3785888	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3809854	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3851784	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3851785	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3851787	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3851792	0.82[CEU][hapmap]
rs4074249	0.83[CEU][hapmap]
rs4381655	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4602097	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4968248	0.91[ASN][1000 genomes]
rs4968250	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4968285	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4968286	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4968287	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4968288	0.94[ASN][1000 genomes]
rs4968290	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4968304	0.81[CEU][hapmap]
rs61671555	0.87[EUR][1000 genomes]
rs62075889	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62075896	0.81[EUR][1000 genomes]
rs6504622	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7213526	0.92[ASN][1000 genomes]
rs7216991	0.83[EUR][1000 genomes]
rs7225428	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7342957	0.94[ASN][1000 genomes]
rs736603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs736604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs740617	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs758391	0.88[CEU][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs758392	0.88[CEU][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs9303532	0.87[EUR][1000 genomes]
rs9889741	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9889762	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9893713	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9898527	0.87[EUR][1000 genomes]
rs9898981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9901977	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9910899	0.87[EUR][1000 genomes]
rs9911366	0.87[EUR][1000 genomes]
rs9911967	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9912794	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3492820	chr17:44174959-45161556	Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3492821	chr17:44174959-45161556	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	esv3502492	chr17:44305975-45169159	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	esv3502493	chr17:44305975-45169159	Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv531823	chr17:44485771-45067769	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv908562	chr17:44828931-45102413	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv949295	chr17:44836653-45080757	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1067211	chr17:44979111-45057620	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
9	nsv543378	chr17:44979111-45057620	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
10	nsv833466	chr17:45020360-45204537	Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3851786	MYL4	cis	multi-tissue	Pritchard
rs3851786	GOSR2	Cis_1M	lymphoblastoid	RTeQTL
rs3851786	GOSR2	cis	normal skin	skin_eQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45021800-45051800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr17:45027400-45054000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr17:45028600-45048800	Weak transcription	Esophagus	oesophagus
4	chr17:45036400-45052400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr17:45036600-45054400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr17:45037400-45055800	Weak transcription	Aorta	Aorta
7	chr17:45037800-45052200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr17:45038000-45052600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr17:45040200-45047800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr17:45040200-45055600	Weak transcription	Pancreas	Pancrea
11	chr17:45042800-45051200	Weak transcription	Fetal Muscle Leg	muscle
12	chr17:45042800-45052800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr17:45043000-45049600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr17:45043000-45054000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr17:45044000-45049600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr17:45044400-45047000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr17:45044600-45049600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr17:45045000-45047000	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr17:45045400-45047000	Strong transcription	Ovary	ovary
20	chr17:45045400-45048200	Strong transcription	Fetal Stomach	stomach
21	chr17:45045400-45049600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr17:45046200-45048000	Weak transcription	Adipose Nuclei	Adipose
23	chr17:45046200-45052600	Weak transcription	HepG2	liver
24	chr17:45046200-45055400	Weak transcription	Spleen	Spleen
25	chr17:45046400-45049600	Weak transcription	Fetal Brain Female	brain
26	chr17:45046400-45050200	Weak transcription	Fetal Intestine Small	intestine
27	chr17:45046600-45048800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr17:45046600-45049400	Weak transcription	Lung	lung
29	chr17:45046600-45050000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr17:45046800-45052400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr17:45046800-45054000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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