Variant report

Variant	rs2602160
Chromosome Location	chr2:20645506-20645507
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:20645055-20645828	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr2:20645370-20646215	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr2:20645433-20645628	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr2:20645058-20645671	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:20645467-20645577	HepG2	liver:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20549379..20553875-chr2:20644345..20648832,13	MCF-7	breast:
2	chr2:20633992..20655025-chr2:20829429..20854651,127	MCF-7	breast:
3	chr2:20640108..20658716-chr2:20812153..20855311,258	MCF-7	breast:
4	chr2:20644186..20651576-chr2:20790196..20799394,18	MCF-7	breast:
5	chr2:20645492..20647330-chr7:139044300..139046201,2	MCF-7	breast:
6	chr2:20643596..20652981-chr2:20820571..20828990,20	MCF-7	breast:
7	chr2:20592640..20602218-chr2:20644635..20652468,15	MCF-7	breast:
8	chr2:20645423..20650748-chr2:20698837..20705480,9	MCF-7	breast:
9	chr2:20644797..20655251-chr2:20787626..20802274,53	MCF-7	breast:
10	chr2:20645482..20647454-chr9:137444146..137446326,2	MCF-7	breast:
11	chr2:20548847..20552407-chr2:20645405..20649585,5	MCF-7	breast:

No data

Variant related genes	Relation type
RHOB	TF binding region
ENSG00000118960	Chromatin interaction
ENSG00000146963	Chromatin interaction
ENSG00000227150	Chromatin interaction
ENSG00000231948	Chromatin interaction
ENSG00000055917	Chromatin interaction
ENSG00000273391	Chromatin interaction
ENSG00000227047	Chromatin interaction
ENSG00000212171	Chromatin interaction
ENSG00000252216	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2924378	0.95[ASN][1000 genomes]
rs342054	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[ASN][1000 genomes]
rs342055	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs342056	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv455830	chr2:20621404-20659862	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv581166	chr2:20621404-20659862	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
3	nsv873717	chr2:20625174-20756900	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv873718	chr2:20627875-20752152	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv873719	chr2:20628882-20756900	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2602160	AC023137.2	cis	Artery Tibial	GTEx
rs2602160	VSNL1	cis	parietal	SCAN
rs2602160	FAM49A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20625000-20646000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:20639400-20646000	Weak transcription	HSMMtube	muscle
3	chr2:20639600-20646000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:20639600-20646000	Weak transcription	Gastric	stomach
5	chr2:20639600-20646200	Weak transcription	HMEC	breast
6	chr2:20642000-20646200	Weak transcription	K562	blood
7	chr2:20643200-20646200	Enhancers	NHDF-Ad	bronchial
8	chr2:20643400-20646000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:20643400-20646000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr2:20643400-20646000	Enhancers	Fetal Brain Male	brain
11	chr2:20643400-20646000	Enhancers	Fetal Muscle Leg	muscle
12	chr2:20643400-20646200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:20643600-20645600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:20643600-20646000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:20643600-20646000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:20643600-20646000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:20643600-20650000	Active TSS	Right Atrium	heart
18	chr2:20643800-20646000	Weak transcription	Fetal Intestine Large	intestine
19	chr2:20644000-20646000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:20644000-20646200	Weak transcription	Fetal Lung	lung
21	chr2:20644200-20646000	Weak transcription	NH-A	brain
22	chr2:20644400-20645600	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr2:20644400-20645600	Flanking Active TSS	Liver	Liver
24	chr2:20644400-20645600	Flanking Active TSS	Stomach Smooth Muscle	stomach
25	chr2:20644400-20645600	Flanking Active TSS	Hela-S3	cervix
26	chr2:20644400-20646000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:20644400-20646000	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr2:20644400-20646000	Enhancers	Brain Cingulate Gyrus	brain
29	chr2:20644400-20646000	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr2:20644400-20646000	Enhancers	Fetal Muscle Trunk	muscle
31	chr2:20644400-20646000	Enhancers	Placenta	Placenta
32	chr2:20644400-20646000	Enhancers	Pancreas	Pancrea
33	chr2:20644400-20646200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:20644400-20646400	Flanking Active TSS	HUVEC	blood vessel
35	chr2:20644600-20645600	Flanking Active TSS	Rectal Smooth Muscle	rectum
36	chr2:20644600-20646000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:20644600-20646000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:20644600-20646000	Weak transcription	Fetal Brain Female	brain
39	chr2:20644600-20646000	Weak transcription	Fetal Intestine Small	intestine
40	chr2:20644600-20646000	Weak transcription	HSMM	muscle
41	chr2:20644600-20646000	Weak transcription	NHLF	lung
42	chr2:20644600-20646200	Weak transcription	Fetal Kidney	kidney
43	chr2:20644600-20646200	Weak transcription	Small Intestine	intestine
44	chr2:20644600-20647000	Active TSS	Right Ventricle	heart
45	chr2:20644600-20650000	Active TSS	Psoas Muscle	Psoas
46	chr2:20644800-20645600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
47	chr2:20644800-20645600	Flanking Active TSS	Brain Anterior Caudate	brain
48	chr2:20644800-20645600	Flanking Active TSS	Colon Smooth Muscle	Colon
49	chr2:20644800-20646000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:20644800-20646000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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