Variant report

Variant	rs3809854
Chromosome Location	chr17:45029294-45029295
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:45028185..45031544-chr17:45032112..45035486,4	K562	blood:

Extended variants
information (count: 99 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1047779	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1052504	0.99[ASN][1000 genomes]
rs1052586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[AMR][1000 genomes];0.96[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	0.82[ASW][hapmap];0.88[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs11079745	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11079750	0.81[CEU][hapmap]
rs11652318	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654971	0.99[ASN][1000 genomes]
rs11655668	0.86[JPT][hapmap]
rs11656362	1.00[ASN][1000 genomes]
rs11658276	0.97[ASN][1000 genomes]
rs11869840	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12601886	0.99[ASN][1000 genomes]
rs12940071	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1618989	0.98[ASN][1000 genomes]
rs1623402	0.99[ASN][1000 genomes]
rs1662576	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1662577	0.99[ASN][1000 genomes]
rs1662594	0.82[ASW][hapmap];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	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs197926	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[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2003538	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2003539	0.82[AMR][1000 genomes];0.94[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	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2317997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28553405	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2920396	0.99[ASN][1000 genomes]
rs2920397	0.99[ASN][1000 genomes]
rs35707546	0.96[ASN][1000 genomes]
rs3760377	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3785888	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3785889	0.81[CEU][hapmap];0.84[GIH][hapmap]
rs3851784	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851785	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3851787	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4074249	0.80[CEU][hapmap]
rs4381655	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4602097	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4968248	0.96[ASN][1000 genomes]
rs4968250	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968285	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4968286	0.96[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];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968287	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4968288	0.99[ASN][1000 genomes]
rs4968290	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4968304	0.80[CEU][hapmap]
rs61671555	0.88[EUR][1000 genomes]
rs62075889	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62075896	0.82[EUR][1000 genomes]
rs6504622	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7213526	0.97[ASN][1000 genomes]
rs7216991	0.84[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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs736604	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[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs740617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs758391	0.82[ASW][hapmap];0.88[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs758392	0.88[CEU][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs9303532	0.88[EUR][1000 genomes]
rs9889741	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9889762	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];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9893713	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9898527	0.88[EUR][1000 genomes]
rs9898981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9901977	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9910899	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9911366	0.88[EUR][1000 genomes]
rs9911967	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9912794	0.88[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3809854	GOSR2	cis	lymphoblastoid	seeQTL
rs3809854	GOSR2	cis	normal skin	skin_eQTL
rs3809854	C17orf53	cis	parietal	SCAN
rs3809854	GOSR2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45012800-45040000	Weak transcription	Hela-S3	cervix
2	chr17:45020000-45034600	Weak transcription	Dnd41	blood
3	chr17:45021600-45039800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr17:45021800-45051800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr17:45022000-45032800	Weak transcription	Primary B cells from peripheral blood	blood
6	chr17:45022000-45035400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr17:45022000-45039800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr17:45022800-45044400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr17:45022800-45045000	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr17:45023000-45034800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr17:45023000-45045400	Weak transcription	Ovary	ovary
12	chr17:45023200-45037600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr17:45023400-45037200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr17:45024800-45037200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr17:45025000-45035200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr17:45026800-45034600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr17:45027000-45033200	Weak transcription	A549	lung
18	chr17:45027000-45033200	Weak transcription	HepG2	liver
19	chr17:45027000-45034000	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr17:45027000-45035000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr17:45027000-45037200	Weak transcription	Aorta	Aorta
22	chr17:45027000-45039800	Weak transcription	Pancreas	Pancrea
23	chr17:45027200-45033000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr17:45027200-45033200	Weak transcription	Fetal Intestine Small	intestine
25	chr17:45027200-45035400	Weak transcription	Primary B cells from cord blood	blood
26	chr17:45027200-45039800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr17:45027400-45030200	Weak transcription	Spleen	Spleen
28	chr17:45027400-45054000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr17:45027600-45029800	Enhancers	Brain Cingulate Gyrus	brain
30	chr17:45027800-45029400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr17:45027800-45029600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
32	chr17:45028000-45029400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr17:45028000-45030200	Enhancers	Fetal Brain Male	brain
34	chr17:45028000-45044400	Weak transcription	Primary T cells from cord blood	blood
35	chr17:45028400-45029400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr17:45028400-45029400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
37	chr17:45028600-45029600	Weak transcription	Brain Angular Gyrus	brain
38	chr17:45028600-45035200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr17:45028600-45048800	Weak transcription	Esophagus	oesophagus
40	chr17:45028800-45029400	Bivalent Enhancer	Fetal Muscle Leg	muscle
41	chr17:45028800-45029600	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr17:45028800-45029800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr17:45029000-45029400	Enhancers	Brain Hippocampus Middle	brain
44	chr17:45029000-45029800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr17:45029200-45029400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
46	chr17:45029200-45029400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr17:45029200-45029400	Enhancers	Thymus	Thymus
48	chr17:45029200-45035400	Weak transcription	Brain Germinal Matrix	brain
49	chr17:45029200-45037400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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