Variant report

Variant	rs494852
Chromosome Location	chr2:31624836-31624837
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:31610791..31613346-chr2:31624556..31626809,2	MCF-7	breast:
2	chr2:31619044..31622000-chr2:31622543..31624849,2	K562	blood:

Variant related genes	Relation type
ENSG00000158125	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11690596	0.81[CHD][hapmap]
rs1346644	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1366814	0.85[CEU][hapmap]
rs206798	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs206800	0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs206802	1.00[CEU][hapmap];0.88[MEX][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes]
rs206803	1.00[CEU][hapmap];0.88[MEX][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes]
rs206804	1.00[ASW][hapmap];0.80[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];0.89[MEX][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs206805	1.00[ASW][hapmap];0.86[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2268794	0.87[CHD][hapmap]
rs3754838	0.81[CHD][hapmap]
rs7562326	0.81[CHD][hapmap]
rs7594951	0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949028	chr2:31502801-31665108	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv532648	chr2:31591498-32312698	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv456030	chr2:31598823-31820256	Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv456041	chr2:31598823-31820256	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv581269	chr2:31598823-31820256	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv998853	chr2:31601455-31858961	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1005565	chr2:31603134-31868877	Genic enhancers Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1007179	chr2:31616112-31835410	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1005032	chr2:31616112-31867450	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs494852	DPY30	cis	parietal	SCAN
rs494852	EHD3	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31548000-31634600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:31565200-31633000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr2:31574600-31636600	Weak transcription	Colonic Mucosa	Colon
4	chr2:31598400-31639000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:31599600-31636600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:31618000-31625400	Strong transcription	Fetal Intestine Large	intestine
7	chr2:31618000-31627000	Strong transcription	Fetal Intestine Small	intestine
8	chr2:31620000-31627600	Strong transcription	Duodenum Mucosa	Duodenum
9	chr2:31620800-31627400	Strong transcription	Liver	Liver
10	chr2:31623400-31625800	Enhancers	Hela-S3	cervix
11	chr2:31623400-31626200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:31623400-31628000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:31623600-31626000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:31623600-31626000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:31623600-31626000	Enhancers	NHDF-Ad	bronchial
16	chr2:31623800-31625000	Enhancers	NH-A	brain
17	chr2:31623800-31625600	Flanking Active TSS	A549	lung
18	chr2:31623800-31625800	Enhancers	Osteobl	bone
19	chr2:31623800-31626000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:31623800-31626000	Enhancers	NHLF	lung
21	chr2:31623800-31626200	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr2:31624000-31625000	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr2:31624000-31625400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:31624000-31625400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:31624000-31625400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:31624000-31625400	Enhancers	HSMM	muscle
27	chr2:31624000-31625600	Enhancers	Muscle Satellite Cultured Cells	--
28	chr2:31624000-31626000	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr2:31624000-31626200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr2:31624000-31626200	Enhancers	Placenta	Placenta
31	chr2:31624200-31625000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:31624200-31625400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:31624200-31625600	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr2:31624200-31625600	Enhancers	HSMMtube	muscle
35	chr2:31624200-31626000	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr2:31624400-31625200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr2:31624400-31625600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:31624400-31625600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:31624400-31626200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:31624400-31626200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:31624600-31625200	Enhancers	NHEK	skin
42	chr2:31624600-31625800	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr2:31624600-31625800	Enhancers	HMEC	breast
44	chr2:31624800-31625000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:31624800-31625400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:31624800-31626000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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