Variant report

Variant	rs11083616
Chromosome Location	chr19:41865643-41865644
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41865641-41866139	K562	blood:	n/a	n/a
2	POLR2A	chr19:41865631-41866019	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:41865584-41866016	GM12891	blood:	n/a	n/a
4	POLR2A	chr19:41865613-41866225	A549	lung:	n/a	n/a

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	chr19:41859483..41864125-chr19:41864354..41869446,7	MCF-7	breast:

Variant related genes	Relation type
TMEM91	TF binding region
ENSG00000142046	Chromatin interaction
ENSG00000105329	Chromatin interaction
ENSG00000123810	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1025497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1046909	0.81[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs11083617	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666933	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11670143	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11670739	0.83[AMR][1000 genomes]
rs12462166	0.97[ASN][1000 genomes]
rs12983775	0.92[ASN][1000 genomes]
rs1549933	0.98[ASN][1000 genomes]
rs1800469	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1800470	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1963413	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1982072	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2241712	0.99[ASN][1000 genomes]
rs2241713	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241714	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2241715	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2317130	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34503210	0.81[AMR][1000 genomes]
rs4803457	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803458	0.90[ASN][1000 genomes]
rs4803459	0.87[ASN][1000 genomes]
rs7260340	0.83[AMR][1000 genomes]
rs8108357	0.81[AMR][1000 genomes]
rs9797885	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11083616	CCDC114	cis	parietal	SCAN
rs11083616	ZNF45	cis	parietal	SCAN
rs11083616	B3GALT7	cis	multi-tissue	Pritchard
rs11083616	LHB	cis	parietal	SCAN
rs11083616	PSG2	cis	parietal	SCAN
rs11083616	EML2	cis	parietal	SCAN

Chromatin state (count:87 , 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	chr19:41860200-41869000	Weak transcription	Gastric	stomach
3	chr19:41860400-41865800	Enhancers	Primary T cells fromperipheralblood	blood
4	chr19:41860400-41868200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr19:41860400-41868600	Weak transcription	GM12878-XiMat	blood
6	chr19:41860400-41868800	Weak transcription	Hela-S3	cervix
7	chr19:41860400-41869000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:41860400-41869000	Weak transcription	Brain Angular Gyrus	brain
9	chr19:41860400-41869000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr19:41860400-41869200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr19:41860400-41869200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr19:41860400-41869200	Weak transcription	HSMMtube	muscle
13	chr19:41860400-41869200	Weak transcription	HUVEC	blood vessel
14	chr19:41860400-41869200	Weak transcription	NHDF-Ad	bronchial
15	chr19:41860400-41869200	Weak transcription	NHLF	lung
16	chr19:41860400-41869400	Weak transcription	Aorta	Aorta
17	chr19:41860400-41869400	Weak transcription	Ovary	ovary
18	chr19:41860600-41866800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:41860600-41866800	Weak transcription	A549	lung
20	chr19:41860600-41868200	Weak transcription	Fetal Intestine Small	intestine
21	chr19:41860600-41868200	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr19:41860600-41868400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr19:41860600-41868600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr19:41860600-41868800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr19:41860600-41869000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr19:41860600-41869200	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr19:41860600-41869200	Weak transcription	Brain Substantia Nigra	brain
28	chr19:41860600-41869200	Weak transcription	Esophagus	oesophagus
29	chr19:41860600-41869200	Weak transcription	Osteobl	bone
30	chr19:41860800-41868600	Weak transcription	Pancreas	Pancrea
31	chr19:41860800-41869200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr19:41860800-41869200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr19:41860800-41869200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr19:41860800-41869200	Weak transcription	Right Ventricle	heart
35	chr19:41861000-41868400	Weak transcription	Dnd41	blood
36	chr19:41861000-41868600	Weak transcription	Fetal Brain Female	brain
37	chr19:41861000-41869200	Weak transcription	Liver	Liver
38	chr19:41861200-41869200	Weak transcription	Fetal Kidney	kidney
39	chr19:41861400-41869000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr19:41861600-41868400	Weak transcription	K562	blood
41	chr19:41861600-41868800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr19:41862000-41866800	Weak transcription	Fetal Stomach	stomach
43	chr19:41862000-41869000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr19:41862000-41869000	Weak transcription	Brain Anterior Caudate	brain
45	chr19:41862000-41869000	Weak transcription	Brain Hippocampus Middle	brain
46	chr19:41862000-41869200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr19:41863000-41868600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr19:41863000-41868800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr19:41863200-41868200	Weak transcription	Stomach Mucosa	stomach
50	chr19:41863200-41869000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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