Variant report

Variant	rs3785889
Chromosome Location	chr17:45005830-45005831
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:44937329..44939889-chr17:45005323..45007178,2	K562	blood:
2	chr17:45003530..45006692-chr17:45016648..45018948,3	K562	blood:
3	chr17:45004362..45006941-chr17:45070896..45073803,2	MCF-7	breast:
4	chr17:44982234..44984014-chr17:45005166..45007066,2	K562	blood:
5	chr17:44848363..44849947-chr17:45003750..45005877,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1047779	0.84[EUR][1000 genomes]
rs1052586	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs11079745	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs11869840	0.85[CEU][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs12940071	0.84[EUR][1000 genomes]
rs17608961	0.83[EUR][1000 genomes]
rs197925	0.81[GIH][hapmap]
rs197926	0.81[CEU][hapmap];0.84[GIH][hapmap];0.83[EUR][1000 genomes]
rs2003539	0.83[EUR][1000 genomes]
rs2317997	0.80[EUR][1000 genomes]
rs3760377	0.81[EUR][1000 genomes]
rs4968285	0.86[EUR][1000 genomes]
rs4968286	0.85[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs62075889	0.83[EUR][1000 genomes]
rs6504622	0.85[CEU][hapmap];0.84[GIH][hapmap];0.83[EUR][1000 genomes]
rs736603	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs736604	0.81[CEU][hapmap];0.84[GIH][hapmap];0.80[EUR][1000 genomes]
rs740617	0.80[EUR][1000 genomes]
rs9889762	0.85[CEU][hapmap];0.86[GIH][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs9898981	0.80[CEU][hapmap];0.80[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	nsv428672	chr17:44872446-45023425	Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	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
10	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3785889	GOSR2	Cis_1M	lymphoblastoid	RTeQTL
rs3785889	GOSR2	cis	normal skin	skin_eQTL
rs3785889	C17orf53	cis	parietal	SCAN
rs3785889	PLCD3	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45001200-45011400	Weak transcription	Fetal Brain Male	brain
2	chr17:45001400-45006800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr17:45001400-45006800	Weak transcription	Placenta	Placenta
4	chr17:45001400-45007000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr17:45001400-45009400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr17:45001600-45006000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr17:45001600-45008200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr17:45001600-45008200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr17:45001600-45020800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr17:45001800-45006000	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr17:45001800-45007000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr17:45001800-45007200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr17:45001800-45008200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr17:45001800-45008200	Weak transcription	HSMMtube	muscle
15	chr17:45002000-45006200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr17:45002000-45006200	Weak transcription	NH-A	brain
17	chr17:45002000-45006400	Weak transcription	NHDF-Ad	bronchial
18	chr17:45002000-45006600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr17:45002000-45006800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr17:45002000-45007000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr17:45002000-45007000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr17:45002000-45007600	Weak transcription	Brain Substantia Nigra	brain
23	chr17:45002000-45008400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr17:45002000-45008400	Weak transcription	Brain Angular Gyrus	brain
25	chr17:45002000-45021000	Weak transcription	Fetal Heart	heart
26	chr17:45002200-45006000	Weak transcription	Hela-S3	cervix
27	chr17:45002200-45006600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr17:45002200-45006600	Weak transcription	Fetal Kidney	kidney
29	chr17:45002200-45006600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr17:45002200-45006800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr17:45002200-45007000	Weak transcription	Brain Germinal Matrix	brain
32	chr17:45002200-45007200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr17:45002200-45007200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr17:45002200-45007600	Weak transcription	Fetal Lung	lung
35	chr17:45002200-45007600	Weak transcription	A549	lung
36	chr17:45002400-45006800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr17:45002400-45006800	Weak transcription	Brain Hippocampus Middle	brain
38	chr17:45002400-45006800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr17:45002400-45006800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr17:45002400-45007400	Weak transcription	Brain Anterior Caudate	brain
41	chr17:45002600-45007600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr17:45002800-45006200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr17:45002800-45006200	Weak transcription	Thymus	Thymus
44	chr17:45002800-45006800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr17:45002800-45006800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr17:45002800-45006800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr17:45002800-45007000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr17:45002800-45020000	Strong transcription	Fetal Muscle Leg	muscle
49	chr17:45003000-45006400	Weak transcription	Osteobl	bone
50	chr17:45003000-45006800	Weak transcription	Fetal Brain Female	brain

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