Variant report

Variant	rs9889762
Chromosome Location	chr17:45026366-45026367
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45000734..45002965-chr17:45025082..45026604,2	K562	blood:
2	chr17:45008062..45010873-chr17:45025495..45027532,2	K562	blood:
3	chr17:45022010..45024522-chr17:45025395..45027145,2	MCF-7	breast:
4	chr17:45025771..45027862-chr17:45033624..45036978,3	K562	blood:
5	chr17:45000330..45001851-chr17:45026008..45027788,2	MCF-7	breast:
6	chr17:45020585..45022293-chr17:45024783..45026785,2	MCF-7	breast:
7	chr17:45023289..45027019-chr17:45054216..45057045,4	K562	blood:
8	chr17:45025335..45027019-chr17:45054266..45057045,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000263142	Chromatin interaction
ENSG00000261886	Chromatin interaction
ENSG00000262633	Chromatin interaction
ENSG00000179673	Chromatin interaction
ENSG00000108433	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1047779	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1052504	0.99[ASN][1000 genomes]
rs1052586	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10853085	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10853087	0.99[ASN][1000 genomes]
rs11079742	0.85[CEU][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs11079745	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11079750	0.84[CEU][hapmap]
rs11652318	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11654971	0.99[ASN][1000 genomes]
rs11655668	0.86[JPT][hapmap]
rs11656362	0.97[ASN][1000 genomes]
rs11658276	0.97[ASN][1000 genomes]
rs11869840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12601886	0.99[ASN][1000 genomes]
rs12940071	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1618989	0.98[ASN][1000 genomes]
rs1623402	0.99[ASN][1000 genomes]
rs1662576	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1662577	0.99[ASN][1000 genomes]
rs1662594	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1662596	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1662597	0.96[ASN][1000 genomes]
rs17608961	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1838105	0.82[JPT][hapmap]
rs1867237	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs189899	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs197912	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs197913	0.87[ASN][1000 genomes]
rs197915	0.90[ASN][1000 genomes]
rs197917	0.97[ASN][1000 genomes]
rs197918	0.99[ASN][1000 genomes]
rs197919	0.99[ASN][1000 genomes]
rs197922	0.82[JPT][hapmap]
rs197923	0.82[JPT][hapmap]
rs197925	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs197926	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2003538	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2003539	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2072317	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2191033	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2316330	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2317997	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28553405	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2920396	0.99[ASN][1000 genomes]
rs2920397	0.99[ASN][1000 genomes]
rs35707546	0.96[ASN][1000 genomes]
rs3760377	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3785888	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3785889	0.85[CEU][hapmap];0.86[GIH][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs3809854	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3851784	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3851785	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3851786	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]
rs3851787	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3851792	0.83[CEU][hapmap];0.80[TSI][hapmap]
rs4074249	0.84[CEU][hapmap]
rs4381655	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4602097	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4968248	0.96[ASN][1000 genomes]
rs4968250	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4968285	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4968286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968287	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4968288	0.99[ASN][1000 genomes]
rs4968290	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4968304	0.84[CEU][hapmap]
rs61671555	0.84[EUR][1000 genomes]
rs62075889	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62075896	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6504622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7213526	0.97[ASN][1000 genomes]
rs7216991	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7225428	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7342957	0.99[ASN][1000 genomes]
rs736603	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs736604	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs740617	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs758391	0.85[CEU][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs758392	0.85[CEU][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs9303532	0.84[EUR][1000 genomes]
rs9889741	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9893713	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9898527	0.84[EUR][1000 genomes]
rs9898981	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9901977	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9910899	0.84[EUR][1000 genomes]
rs9911366	0.84[EUR][1000 genomes]
rs9911967	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9912794	0.84[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	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9889762	MYL4	cis	multi-tissue	Pritchard
rs9889762	GOSR2	Cis_1M	lymphoblastoid	RTeQTL
rs9889762	PLCD3	cis	parietal	SCAN
rs9889762	C17orf53	cis	parietal	SCAN
rs9889762	GOSR2	cis	multi-tissue	Pritchard
rs9889762	LRRC46	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45012800-45040000	Weak transcription	Hela-S3	cervix
2	chr17:45018200-45028400	Weak transcription	Fetal Brain Female	brain
3	chr17:45018600-45028600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr17:45020000-45034600	Weak transcription	Dnd41	blood
5	chr17:45021200-45028000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr17:45021200-45028400	Weak transcription	Gastric	stomach
7	chr17:45021600-45026400	Weak transcription	Liver	Liver
8	chr17:45021600-45026600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr17:45021600-45028000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr17:45021600-45039800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr17:45021800-45026400	Weak transcription	Colonic Mucosa	Colon
12	chr17:45021800-45026800	Weak transcription	HSMMtube	muscle
13	chr17:45021800-45028000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr17:45021800-45028400	Weak transcription	Brain Germinal Matrix	brain
15	chr17:45021800-45051800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr17:45022000-45026400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr17:45022000-45028000	Weak transcription	Fetal Brain Male	brain
18	chr17:45022000-45029000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr17:45022000-45032800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr17:45022000-45035400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr17:45022000-45039800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr17:45022600-45026400	Weak transcription	Colon Smooth Muscle	Colon
23	chr17:45022600-45027600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr17:45022800-45026400	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr17:45022800-45026400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr17:45022800-45026800	Weak transcription	Brain Angular Gyrus	brain
27	chr17:45022800-45027000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr17:45022800-45028000	Weak transcription	Right Atrium	heart
29	chr17:45022800-45028200	Weak transcription	Lung	lung
30	chr17:45022800-45044400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr17:45022800-45045000	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr17:45023000-45027000	Weak transcription	Left Ventricle	heart
33	chr17:45023000-45027800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr17:45023000-45028000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr17:45023000-45028600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr17:45023000-45034800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr17:45023000-45045400	Weak transcription	Ovary	ovary
38	chr17:45023200-45028200	Weak transcription	Right Ventricle	heart
39	chr17:45023200-45037600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr17:45023400-45026800	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr17:45023400-45028800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr17:45023400-45029000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr17:45023400-45037200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr17:45024600-45026400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr17:45024800-45028800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr17:45024800-45037200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr17:45025000-45028000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr17:45025000-45028800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr17:45025000-45035200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr17:45025200-45026600	Weak transcription	Fetal Muscle Leg	muscle

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