Variant report

Variant	rs1982072
Chromosome Location	chr19:41864509-41864510
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41864475-41864791	HepG2	liver:	n/a	n/a
2	SPI1	chr19:41864214-41864608	HL-60	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:41864348..41865900-chr19:41868639..41870352,2	MCF-7	breast:
2	chr19:41830987..41833840-chr19:41863132..41865918,2	MCF-7	breast:
3	chr19:41861604..41864575-chr19:41933607..41936595,2	MCF-7	breast:
4	chr19:41861983..41864638-chr19:41901106..41902845,2	K562	blood:
5	chr19:41859483..41864125-chr19:41864354..41869446,7	MCF-7	breast:

No data

Variant related genes	Relation type
TGFB1	TF binding region
ENSG00000142046	Chromatin interaction
ENSG00000123810	Chromatin interaction
ENSG00000177191	Chromatin interaction
ENSG00000105329	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1025497	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1046909	0.82[JPT][hapmap]
rs11083616	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11083617	0.98[ASN][1000 genomes]
rs11666933	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs11668109	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11670143	0.99[ASN][1000 genomes]
rs12462166	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12983775	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1549933	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1800469	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1800470	0.94[ASN][1000 genomes]
rs1963413	0.96[ASN][1000 genomes]
rs2241712	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2241713	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2241714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2241715	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2317130	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803457	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs4803458	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803459	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9797885	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1802868	chr19:41856886-41869392	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
2	nsv521311	chr19:41856886-41882712	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1982072	MGC4093	cis	multi-tissue	Pritchard

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41859800-41868200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr19:41860200-41864800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr19:41860200-41865000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr19:41860200-41869000	Weak transcription	Gastric	stomach
5	chr19:41860400-41864800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr19:41860400-41865800	Enhancers	Primary T cells fromperipheralblood	blood
7	chr19:41860400-41868200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr19:41860400-41868600	Weak transcription	GM12878-XiMat	blood
9	chr19:41860400-41868800	Weak transcription	Hela-S3	cervix
10	chr19:41860400-41869000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:41860400-41869000	Weak transcription	Brain Angular Gyrus	brain
12	chr19:41860400-41869000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr19:41860400-41869200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr19:41860400-41869200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr19:41860400-41869200	Weak transcription	HSMMtube	muscle
16	chr19:41860400-41869200	Weak transcription	HUVEC	blood vessel
17	chr19:41860400-41869200	Weak transcription	NHDF-Ad	bronchial
18	chr19:41860400-41869200	Weak transcription	NHLF	lung
19	chr19:41860400-41869400	Weak transcription	Aorta	Aorta
20	chr19:41860400-41869400	Weak transcription	Ovary	ovary
21	chr19:41860600-41864600	Enhancers	Primary hematopoietic stem cells	blood
22	chr19:41860600-41864600	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr19:41860600-41864800	Enhancers	Fetal Thymus	thymus
24	chr19:41860600-41866800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr19:41860600-41866800	Weak transcription	A549	lung
26	chr19:41860600-41868200	Weak transcription	Fetal Intestine Small	intestine
27	chr19:41860600-41868200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr19:41860600-41868400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr19:41860600-41868600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr19:41860600-41868800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr19:41860600-41869000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr19:41860600-41869200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr19:41860600-41869200	Weak transcription	Brain Substantia Nigra	brain
34	chr19:41860600-41869200	Weak transcription	Esophagus	oesophagus
35	chr19:41860600-41869200	Weak transcription	Osteobl	bone
36	chr19:41860800-41868600	Weak transcription	Pancreas	Pancrea
37	chr19:41860800-41869200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr19:41860800-41869200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr19:41860800-41869200	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr19:41860800-41869200	Weak transcription	Right Ventricle	heart
41	chr19:41861000-41868400	Weak transcription	Dnd41	blood
42	chr19:41861000-41868600	Weak transcription	Fetal Brain Female	brain
43	chr19:41861000-41869200	Weak transcription	Liver	Liver
44	chr19:41861200-41869200	Weak transcription	Fetal Kidney	kidney
45	chr19:41861400-41869000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr19:41861600-41868400	Weak transcription	K562	blood
47	chr19:41861600-41868800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr19:41862000-41866800	Weak transcription	Fetal Stomach	stomach
49	chr19:41862000-41869000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr19:41862000-41869000	Weak transcription	Brain Anterior Caudate	brain

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