Variant report

Variant	rs62139669
Chromosome Location	chr2:47613699-47613700
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47560223..47562365-chr2:47611010..47614191,3	MCF-7	breast:
2	chr2:47560958..47563782-chr2:47613273..47615976,2	MCF-7	breast:
3	chr2:47595232..47598426-chr2:47612050..47615406,4	MCF-7	breast:
4	chr2:47598793..47602233-chr2:47611835..47614827,3	K562	blood:
5	chr2:47608775..47611521-chr2:47612524..47615427,2	K562	blood:
6	chr2:47607783..47609301-chr2:47611635..47613881,2	K562	blood:
7	chr2:47595342..47597838-chr2:47611988..47613906,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119888	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs17217828	0.82[AMR][1000 genomes]
rs17224199	0.82[AMR][1000 genomes]
rs62138458	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62139664	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62139709	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62139710	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47597200-47615000	Weak transcription	Esophagus	oesophagus
2	chr2:47597200-47619800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:47597400-47614800	Weak transcription	HMEC	breast
4	chr2:47597400-47617000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:47597400-47629400	Weak transcription	NHEK	skin
6	chr2:47597600-47615400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:47600200-47617800	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr2:47600400-47616800	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:47600600-47614000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:47600600-47617200	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:47600800-47614000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:47601000-47614200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:47601200-47614600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr2:47601200-47616800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr2:47601200-47629400	Weak transcription	Stomach Mucosa	stomach
16	chr2:47603200-47619000	Weak transcription	K562	blood
17	chr2:47604800-47617000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:47604800-47628800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:47605200-47629000	Weak transcription	Brain Germinal Matrix	brain
20	chr2:47607400-47614800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:47607800-47615400	Weak transcription	HepG2	liver
22	chr2:47607800-47624000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:47608000-47614600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:47608000-47629000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr2:47609200-47618200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr2:47609200-47619600	Strong transcription	Fetal Intestine Large	intestine
27	chr2:47609800-47618800	Weak transcription	Pancreas	Pancrea
28	chr2:47609800-47619600	Weak transcription	Gastric	stomach
29	chr2:47609800-47629200	Weak transcription	Fetal Stomach	stomach
30	chr2:47610200-47615400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr2:47611000-47614000	Strong transcription	Duodenum Mucosa	Duodenum
32	chr2:47611600-47613800	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr2:47611600-47617200	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr2:47611800-47619400	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr2:47612000-47629000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:47612200-47614600	Weak transcription	Colonic Mucosa	Colon
37	chr2:47612400-47614000	Weak transcription	Fetal Intestine Small	intestine
38	chr2:47613000-47613800	Strong transcription	Fetal Kidney	kidney
39	chr2:47613200-47616400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:47613400-47619200	Weak transcription	H9 Cell Line	embryonic stem cell

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