Variant report

Variant	rs179570
Chromosome Location	chr19:36251326-36251327
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:36251324-36251334	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:36247404..36252021-chr19:36265348..36272678,7	MCF-7	breast:
2	chr19:36248580..36254743-chr19:36274692..36280659,6	K562	blood:
3	chr19:36206099..36210841-chr19:36246614..36251827,8	MCF-7	breast:
4	chr19:36238866..36244880-chr19:36246037..36252437,21	MCF-7	breast:
5	chr19:36247584..36253409-chr19:36264102..36268750,7	K562	blood:

No data

Variant related genes	Relation type
C19orf55	TF binding region
HSPB6	TF binding region
ENSG00000267796	Chromatin interaction
ENSG00000004777	Chromatin interaction
ENSG00000272333	Chromatin interaction
ENSG00000267439	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs107068	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1269214	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs173003	0.82[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs2242522	0.96[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2242523	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2285421	0.85[CEU][hapmap]
rs231238	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs231244	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs231588	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs231591	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs231592	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55939240	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs614225	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs807478	0.89[EUR][1000 genomes]
rs807479	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[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9917056	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911630	chr19:36149761-36290977	Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
3	nsv458566	chr19:36156588-36265508	Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv579422	chr19:36156588-36265508	Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
5	nsv911631	chr19:36169285-36290977	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv911632	chr19:36174176-36288297	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv911633	chr19:36206050-36283847	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
8	nsv911634	chr19:36206050-36290977	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
9	nsv543996	chr19:36210269-36265431	Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv1057830	chr19:36210269-36279794	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv543997	chr19:36210269-36279794	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
12	nsv911635	chr19:36217333-36283847	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
13	nsv458567	chr19:36221051-36283847	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
14	nsv579423	chr19:36221051-36283847	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
15	nsv911636	chr19:36240960-36290977	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs179570	U2AF1L4	cis	multi-tissue	Pritchard
rs179570	ZBTB32	cis	Nerve Tibial	GTEx
rs179570	ZBTB32	cis	lung	GTEx
rs179570	U2AF1L3	cis	multi-tissue	Pritchard
rs179570	ZBTB32	cis	Thyroid	GTEx
rs179570	COX6B1	cis	Muscle Skeletal	GTEx
rs179570	COX6B1	cis	Heart Left Ventricle	GTEx
rs179570	RN7SL765P	cis	Muscle Skeletal	GTEx
rs179570	AC002398.13	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36249400-36251400	Enhancers	Spleen	Spleen
2	chr19:36249600-36251400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr19:36249600-36251800	Weak transcription	Ovary	ovary
4	chr19:36249600-36252600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr19:36249800-36251800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:36249800-36251800	Weak transcription	HSMMtube	muscle
7	chr19:36249800-36255000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr19:36249800-36265600	Weak transcription	Right Atrium	heart
9	chr19:36249800-36265800	Weak transcription	Fetal Kidney	kidney
10	chr19:36250000-36251400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr19:36250000-36251800	Weak transcription	Brain Hippocampus Middle	brain
12	chr19:36250000-36252200	Genic enhancers	Fetal Muscle Trunk	muscle
13	chr19:36250000-36252400	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr19:36250000-36252800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr19:36250000-36254800	Weak transcription	Adipose Nuclei	Adipose
16	chr19:36250000-36255000	Weak transcription	Esophagus	oesophagus
17	chr19:36250000-36255800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr19:36250000-36258400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr19:36250000-36265600	Weak transcription	Brain Substantia Nigra	brain
20	chr19:36250200-36251400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr19:36250200-36251800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr19:36250200-36252000	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr19:36250200-36252800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr19:36250200-36252800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr19:36250200-36252800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr19:36250200-36255200	Weak transcription	Primary B cells from cord blood	blood
27	chr19:36250200-36265400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr19:36250400-36251400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr19:36250400-36251400	Genic enhancers	Thymus	Thymus
30	chr19:36250400-36251800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr19:36250400-36251800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr19:36250400-36251800	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr19:36250400-36251800	Weak transcription	NHDF-Ad	bronchial
34	chr19:36250400-36252800	Weak transcription	Colonic Mucosa	Colon
35	chr19:36250400-36252800	Weak transcription	Gastric	stomach
36	chr19:36250400-36252800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr19:36250400-36253000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr19:36250400-36253000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr19:36250400-36253400	Strong transcription	Fetal Lung	lung
40	chr19:36250400-36255000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr19:36250400-36260200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr19:36250400-36265400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr19:36250400-36265600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr19:36250400-36265600	Weak transcription	Psoas Muscle	Psoas
45	chr19:36250400-36265800	Weak transcription	Small Intestine	intestine
46	chr19:36250400-36266000	Weak transcription	Aorta	Aorta
47	chr19:36250600-36251400	Genic enhancers	Fetal Thymus	thymus
48	chr19:36250600-36251600	Weak transcription	NH-A	brain
49	chr19:36250600-36251800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr19:36250600-36251800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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