Variant report

Variant	rs4953497
Chromosome Location	chr2:47599141-47599142
allele	A/C
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:6)
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	TAL1	chr2:47599108-47599211	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47592763..47599978-chr2:47628456..47631890,7	K562	blood:
2	chr2:47597774..47599287-chr2:47627700..47629210,2	MCF-7	breast:
3	chr2:47598530..47600190-chr2:47604958..47607928,2	K562	blood:
4	chr2:47401904..47404708-chr2:47598417..47601115,2	MCF-7	breast:
5	chr2:47560518..47577182-chr2:47592669..47600258,43	MCF-7	breast:
6	chr2:47559485..47574826-chr2:47594341..47605593,65	MCF-7	breast:

No data

Variant related genes	Relation type
EPCAM	TF binding region
ENSG00000095002	Chromatin interaction
ENSG00000234690	Chromatin interaction
ENSG00000119888	Chromatin interaction
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs17036537	0.88[CEU][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17036544	0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.98[ASN][1000 genomes]
rs35079997	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3923560	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4399765	0.96[ASN][1000 genomes]
rs4952884	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4952886	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4953495	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4953498	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55931899	0.96[ASN][1000 genomes]
rs56368712	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60417954	0.93[ASN][1000 genomes]
rs61348463	0.95[ASN][1000 genomes]
rs61493074	0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs62138459	0.90[ASN][1000 genomes]
rs66617176	0.94[ASN][1000 genomes]
rs72808419	0.83[AMR][1000 genomes]
rs72808422	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72810397	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72812303	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72812306	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72812307	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7558107	0.96[AFR][1000 genomes];0.90[AMR][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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv999576	chr2:47506116-47773960	Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv1009586	chr2:47552706-47621487	Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
6	nsv520660	chr2:47590034-47601106	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47595800-47599200	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr2:47596000-47599400	Active TSS	K562	blood
3	chr2:47596000-47601000	Active TSS	Rectal Smooth Muscle	rectum
4	chr2:47596600-47600400	Active TSS	Small Intestine	intestine
5	chr2:47596800-47600000	Active TSS	Sigmoid Colon	Sigmoid Colon
6	chr2:47597000-47600600	Weak transcription	A549	lung
7	chr2:47597200-47600800	Weak transcription	Brain Angular Gyrus	brain
8	chr2:47597200-47610600	Weak transcription	Right Atrium	heart
9	chr2:47597200-47615000	Weak transcription	Esophagus	oesophagus
10	chr2:47597200-47619800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:47597400-47599200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:47597400-47600600	Weak transcription	Fetal Lung	lung
13	chr2:47597400-47600800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:47597400-47601000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:47597400-47601000	Weak transcription	Brain Anterior Caudate	brain
16	chr2:47597400-47601000	Weak transcription	Brain Substantia Nigra	brain
17	chr2:47597400-47601200	Active TSS	Colonic Mucosa	Colon
18	chr2:47597400-47602600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr2:47597400-47604000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:47597400-47607000	Weak transcription	Gastric	stomach
21	chr2:47597400-47614800	Weak transcription	HMEC	breast
22	chr2:47597400-47617000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:47597400-47629400	Weak transcription	NHEK	skin
24	chr2:47597600-47599400	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 31	rectum
25	chr2:47597600-47615400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:47598000-47600000	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr2:47598400-47599200	Active TSS	Fetal Stomach	stomach
28	chr2:47598400-47599200	Active TSS	Stomach Mucosa	stomach
29	chr2:47598400-47599400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
30	chr2:47598400-47603400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr2:47598400-47604200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:47598600-47599200	Genic enhancers	HepG2	liver
33	chr2:47598600-47601600	Weak transcription	Fetal Brain Male	brain
34	chr2:47598600-47604200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr2:47598600-47607000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:47598600-47607000	Weak transcription	Pancreas	Pancrea
37	chr2:47598600-47607200	Weak transcription	Brain Hippocampus Middle	brain
38	chr2:47598600-47613000	Weak transcription	Lung	lung
39	chr2:47598800-47599400	Genic enhancers	HUES48 Cell Line	embryonic stem cell
40	chr2:47598800-47599400	Active TSS	Fetal Intestine Small	intestine
41	chr2:47598800-47600000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:47598800-47601000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr2:47598800-47601000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr2:47598800-47601200	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr2:47599000-47599400	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr2:47599000-47600400	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr2:47599000-47600600	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr2:47599000-47601200	Active TSS	Duodenum Mucosa	Duodenum
49	chr2:47599000-47601400	Active TSS	Fetal Intestine Large	intestine
50	chr2:47599000-47606200	Weak transcription	Fetal Kidney	kidney

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