Variant report

Variant	rs685200
Chromosome Location	chr19:53041107-53041108
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	chr19:53039676..53041332-chr19:53072309..53073853,2	MCF-7	breast:
2	chr19:53039880..53042500-chr19:53052327..53054340,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167562	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs162277	0.83[EUR][1000 genomes]
rs162278	0.83[EUR][1000 genomes]
rs1676153	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2045754	0.81[ASN][1000 genomes]
rs2608513	0.92[ASN][1000 genomes]
rs2608522	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2608527	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2615586	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2615587	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2615588	0.97[ASN][1000 genomes]
rs2617795	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2633502	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2633513	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2633514	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2633517	0.88[ASN][1000 genomes]
rs2925976	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs326439	0.89[ASN][1000 genomes]
rs326440	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs326441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs326442	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs326443	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs326444	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs326446	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs326447	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs326448	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs326449	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs326458	0.83[CHB][hapmap];0.83[EUR][1000 genomes]
rs329967	0.83[GIH][hapmap]
rs368922	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs369806	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs375267	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs376595	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs396663	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs400709	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs402737	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs410046	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs413751	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs413814	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs417599	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs422195	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs429367	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs434709	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs434788	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs439618	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs440545	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs441549	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs441850	0.88[CEU][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs445500	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs449671	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4802971	0.90[ASN][1000 genomes]
rs4802972	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs520958	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs521703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs529698	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs606521	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs606538	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs606914	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs607477	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62117197	0.91[ASN][1000 genomes]
rs62117198	0.92[ASN][1000 genomes]
rs62117199	0.93[ASN][1000 genomes]
rs62119359	0.88[ASN][1000 genomes]
rs642493	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs653483	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs656541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs666356	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs668882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs688646	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs781129	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs92520	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9676916	0.95[CHB][hapmap];0.95[JPT][hapmap]

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	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv580026	chr19:52937100-53059872	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1063648	chr19:52938131-53041119	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv978841	chr19:52983057-53088237	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1066717	chr19:52993620-53041995	Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1064342	chr19:52996710-53041119	ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1055859	chr19:53001299-53041119	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1060656	chr19:53001299-53041995	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv510772	chr19:53037211-53103470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs685200	ZNF582	cis	cerebellum	SCAN
rs685200	SHISA7	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53032200-53057000	Weak transcription	Hela-S3	cervix
2	chr19:53032600-53049800	Weak transcription	HepG2	liver
3	chr19:53037600-53051800	Weak transcription	K562	blood
4	chr19:53039000-53052200	Weak transcription	Fetal Brain Male	brain
5	chr19:53039200-53056000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
6	chr19:53039600-53052000	Weak transcription	HSMMtube	muscle
7	chr19:53039800-53046000	Weak transcription	Stomach Mucosa	stomach
8	chr19:53039800-53046200	Weak transcription	Aorta	Aorta
9	chr19:53039800-53050600	Weak transcription	Fetal Lung	lung
10	chr19:53039800-53051600	Weak transcription	Brain Substantia Nigra	brain
11	chr19:53039800-53051600	Weak transcription	Fetal Kidney	kidney
12	chr19:53040000-53042400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr19:53040000-53043200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr19:53040000-53045000	Weak transcription	NH-A	brain
15	chr19:53040000-53046000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr19:53040000-53046200	Weak transcription	Brain Anterior Caudate	brain
17	chr19:53040000-53046200	Weak transcription	Left Ventricle	heart
18	chr19:53040000-53046600	Weak transcription	Gastric	stomach
19	chr19:53040000-53046600	Weak transcription	Ovary	ovary
20	chr19:53040000-53046800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr19:53040000-53046800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr19:53040000-53046800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:53040000-53046800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr19:53040000-53047400	Weak transcription	Brain Hippocampus Middle	brain
25	chr19:53040000-53047400	Weak transcription	HSMM	muscle
26	chr19:53040000-53047600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr19:53040000-53051600	Weak transcription	Brain Angular Gyrus	brain
28	chr19:53040000-53051800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr19:53040000-53052000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:53040000-53052200	Weak transcription	Psoas Muscle	Psoas
31	chr19:53040000-53054400	Weak transcription	Fetal Heart	heart
32	chr19:53040200-53041400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr19:53040200-53041800	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr19:53040200-53041800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr19:53040200-53042400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr19:53040200-53042400	Weak transcription	Colonic Mucosa	Colon
37	chr19:53040200-53042600	Weak transcription	Fetal Stomach	stomach
38	chr19:53040200-53042800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr19:53040200-53043000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr19:53040200-53043200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr19:53040200-53043200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr19:53040200-53044600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr19:53040200-53044600	Weak transcription	Fetal Muscle Leg	muscle
44	chr19:53040200-53044800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr19:53040200-53046000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr19:53040200-53046200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr19:53040200-53046200	Weak transcription	Fetal Thymus	thymus
48	chr19:53040200-53046200	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr19:53040200-53046200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr19:53040200-53046400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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