Variant report

Variant	rs62138457
Chromosome Location	chr2:47583704-47583705
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	chr2:47572231..47576038-chr2:47579794..47584297,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119888	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs17036622	0.84[EUR][1000 genomes]
rs17217828	0.85[EUR][1000 genomes]
rs17218055	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17218104	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17224199	0.85[EUR][1000 genomes]
rs17224444	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56116962	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62138455	1.00[AMR][1000 genomes]
rs62139661	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62139662	0.95[EUR][1000 genomes]
rs62139666	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62139715	0.85[EUR][1000 genomes]
rs62139722	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62139723	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62140871	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv524003	chr2:47543245-47590034	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv581756	chr2:47552706-47590930	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	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
8	esv3416811	chr2:47583123-47583731	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47574400-47584400	Weak transcription	Right Atrium	heart
2	chr2:47574800-47584200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:47575000-47586600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:47578200-47589600	Enhancers	Fetal Intestine Small	intestine
5	chr2:47579400-47584000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:47579400-47584600	Weak transcription	Fetal Lung	lung
7	chr2:47579600-47584200	Weak transcription	Fetal Stomach	stomach
8	chr2:47580200-47589600	Enhancers	Fetal Intestine Large	intestine
9	chr2:47580600-47588400	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr2:47581000-47584800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:47581200-47584200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr2:47581400-47584400	Weak transcription	Spleen	Spleen
13	chr2:47581600-47584200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:47581800-47584200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:47581800-47584200	Weak transcription	Small Intestine	intestine
16	chr2:47581800-47584400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr2:47581800-47584400	Weak transcription	Colonic Mucosa	Colon
18	chr2:47582000-47584000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:47582000-47584200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:47582000-47584200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:47582000-47584200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:47582200-47584200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:47582200-47584200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:47582400-47584000	Weak transcription	Osteobl	bone
25	chr2:47582400-47584400	Weak transcription	NHLF	lung
26	chr2:47582400-47585200	Enhancers	K562	blood
27	chr2:47582400-47588200	Weak transcription	NHDF-Ad	bronchial
28	chr2:47582600-47584000	Weak transcription	HMEC	breast
29	chr2:47582600-47584200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:47582600-47584400	Weak transcription	NH-A	brain
31	chr2:47582800-47583800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:47582800-47583800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:47582800-47583800	Weak transcription	A549	lung
34	chr2:47582800-47583800	Weak transcription	HepG2	liver
35	chr2:47582800-47584200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr2:47582800-47584400	Weak transcription	NHEK	skin
37	chr2:47583000-47584000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:47583000-47584400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr2:47583000-47584400	Weak transcription	HUVEC	blood vessel
40	chr2:47583000-47586600	Weak transcription	Stomach Mucosa	stomach
41	chr2:47583200-47584200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr2:47583200-47585200	Enhancers	Duodenum Mucosa	Duodenum

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