Variant report

Variant	rs11083473
Chromosome Location	chr19:39179934-39179935
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39150082..39153309-chr19:39178166..39180062,3	MCF-7	breast:
2	chr19:39174872..39176720-chr19:39177328..39180654,3	K562	blood:
3	chr19:39176509..39181573-chr19:39186750..39192510,7	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10403540	0.94[JPT][hapmap];1.00[YRI][hapmap]
rs10415219	0.83[CHD][hapmap];0.80[JPT][hapmap]
rs10424568	0.92[CEU][hapmap];0.83[TSI][hapmap]
rs10426809	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11083475	0.80[JPT][hapmap];0.88[YRI][hapmap]
rs11665964	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs16972767	0.83[CHD][hapmap];0.80[JPT][hapmap]
rs2279144	0.81[CHD][hapmap]
rs28377909	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3745859	0.85[CHD][hapmap]
rs3786835	0.80[JPT][hapmap];0.88[YRI][hapmap]
rs3786845	0.81[CHD][hapmap]
rs3786851	0.83[CHD][hapmap];0.80[JPT][hapmap];0.82[YRI][hapmap]
rs749701	0.88[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs755690	0.82[EUR][1000 genomes]
rs883433	0.83[CHD][hapmap];0.80[JPT][hapmap];0.82[YRI][hapmap]
rs9304577	0.82[CEU][hapmap]
rs979971	0.82[CHD][hapmap];0.80[JPT][hapmap]
rs979972	0.80[JPT][hapmap];0.88[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
5	nsv817834	chr19:39174332-39237950	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv911668	chr19:39174669-39291771	Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	esv1826260	chr19:39178364-39248836	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11083473	ERCC1	cis	cerebellum	SCAN
rs11083473	RPS16	cis	parietal	SCAN
rs11083473	LGALS17A	cis	cerebellum	SCAN
rs11083473	EXOSC5	cis	parietal	SCAN
rs11083473	PSG3	cis	parietal	SCAN
rs11083473	ZNF526	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39164400-39200200	Genic enhancers	Fetal Intestine Small	intestine
2	chr19:39164800-39183800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr19:39167400-39180800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:39169200-39181000	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr19:39170000-39183400	Enhancers	Placenta	Placenta
6	chr19:39170200-39180000	Enhancers	Adipose Nuclei	Adipose
7	chr19:39173000-39180200	Enhancers	NHDF-Ad	bronchial
8	chr19:39174800-39182800	Weak transcription	Dnd41	blood
9	chr19:39175000-39181000	Weak transcription	Aorta	Aorta
10	chr19:39175000-39181200	Enhancers	Fetal Heart	heart
11	chr19:39175600-39180000	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr19:39175600-39182800	Genic enhancers	NHEK	skin
13	chr19:39176200-39180200	Genic enhancers	HSMM	muscle
14	chr19:39176400-39182600	Weak transcription	Ovary	ovary
15	chr19:39176800-39180000	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr19:39176800-39182000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr19:39176800-39182000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr19:39176800-39182800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr19:39177000-39180000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr19:39177000-39180200	Enhancers	HUVEC	blood vessel
21	chr19:39177000-39183000	Weak transcription	Fetal Brain Female	brain
22	chr19:39177200-39180800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr19:39177200-39182400	Weak transcription	Brain Angular Gyrus	brain
24	chr19:39177200-39182600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr19:39177200-39195000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr19:39177400-39180200	Enhancers	Duodenum Mucosa	Duodenum
27	chr19:39177400-39180200	Enhancers	HepG2	liver
28	chr19:39177400-39180600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr19:39177400-39180800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:39177400-39180800	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr19:39177400-39180800	Enhancers	HMEC	breast
32	chr19:39177400-39181600	Weak transcription	Brain Anterior Caudate	brain
33	chr19:39177400-39181600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr19:39177400-39181600	Weak transcription	Brain Substantia Nigra	brain
35	chr19:39177400-39182200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr19:39177400-39182400	Weak transcription	Fetal Lung	lung
37	chr19:39177400-39182400	Weak transcription	Gastric	stomach
38	chr19:39177400-39182600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr19:39177400-39182600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr19:39177400-39183400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr19:39177600-39180000	Weak transcription	Fetal Stomach	stomach
42	chr19:39177600-39180000	Enhancers	NHLF	lung
43	chr19:39177600-39180200	Enhancers	Hela-S3	cervix
44	chr19:39177600-39180400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr19:39177600-39180600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr19:39177600-39180800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr19:39177600-39181000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr19:39177600-39182400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr19:39177600-39182600	Weak transcription	Colonic Mucosa	Colon
50	chr19:39177600-39182800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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