Variant report

Variant	rs12472478
Chromosome Location	chr2:20779382-20779383
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20777398..20780363-chr2:20792130..20794608,2	MCF-7	breast:
2	chr2:20673517..20675225-chr2:20778394..20780354,2	MCF-7	breast:
3	chr2:20777247..20781087-chr2:20782458..20786081,5	K562	blood:
4	chr2:20664924..20667934-chr2:20777556..20780555,3	MCF-7	breast:
5	chr2:20100218..20102448-chr2:20777945..20780505,2	K562	blood:
6	chr2:20777789..20780759-chr2:20800338..20803588,3	K562	blood:
7	chr2:20646828..20648373-chr2:20777699..20779785,2	MCF-7	breast:
8	chr2:20644778..20652349-chr2:20775724..20782509,25	MCF-7	breast:
9	chr2:20778568..20780393-chr2:20788647..20790853,2	K562	blood:
10	chr2:20775386..20780947-chr2:20790998..20795393,7	K562	blood:
11	chr2:20772999..20776929-chr2:20778925..20783592,5	MCF-7	breast:
12	chr2:20777677..20780481-chr2:20791638..20794768,3	MCF-7	breast:
13	chr2:20777436..20779851-chr2:20800410..20803316,2	K562	blood:
14	chr2:20778242..20781356-chr2:20782083..20785108,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000231948	Chromatin interaction
ENSG00000143878	Chromatin interaction
ENSG00000228950	Chromatin interaction
ENSG00000183891	Chromatin interaction
ENSG00000271991	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10166792	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10177787	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10177834	0.87[CEU][hapmap];0.86[CHB][hapmap]
rs10190705	0.86[ASN][1000 genomes]
rs10195324	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10195722	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10200207	0.85[ASN][1000 genomes]
rs11096676	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11096677	0.90[ASN][1000 genomes]
rs11096679	0.86[CHB][hapmap]
rs1123781	0.88[ASN][1000 genomes]
rs11691255	0.86[ASN][1000 genomes]
rs11885969	0.86[CHB][hapmap]
rs11897611	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12621527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13013281	0.85[CHB][hapmap]
rs13031724	0.85[CHB][hapmap]
rs13422371	0.86[ASN][1000 genomes]
rs16987857	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16987878	0.92[JPT][hapmap]
rs16987880	0.93[JPT][hapmap]
rs16987884	0.93[JPT][hapmap]
rs1809132	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2882035	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2882036	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4666315	0.90[ASN][1000 genomes]
rs4666426	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4666427	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4666428	0.87[EUR][1000 genomes]
rs4666429	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4666430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666431	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666436	0.85[CHB][hapmap]
rs56129345	0.84[ASN][1000 genomes]
rs6715159	0.86[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6722960	0.87[CEU][hapmap];0.86[CHB][hapmap]
rs72782365	0.83[ASN][1000 genomes]
rs766474	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs921599	0.86[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv833548	chr2:20682073-20864078	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1012037	chr2:20770850-20824893	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535598	chr2:20770850-20824893	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20765600-20780800	Enhancers	Adipose Nuclei	Adipose
2	chr2:20765800-20786200	Enhancers	HUVEC	blood vessel
3	chr2:20766800-20780800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr2:20766800-20781000	Enhancers	Left Ventricle	heart
5	chr2:20767000-20781000	Enhancers	Right Atrium	heart
6	chr2:20767800-20782600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:20769400-20780000	Enhancers	Fetal Intestine Large	intestine
8	chr2:20769800-20781000	Enhancers	Fetal Muscle Leg	muscle
9	chr2:20772600-20781000	Enhancers	Placenta	Placenta
10	chr2:20772600-20785800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:20772800-20779400	Weak transcription	Liver	Liver
12	chr2:20772800-20780800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:20773000-20781000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:20773400-20781200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr2:20773600-20780000	Enhancers	Spleen	Spleen
16	chr2:20773600-20780200	Enhancers	Fetal Heart	heart
17	chr2:20773600-20781000	Enhancers	Lung	lung
18	chr2:20774600-20781000	Enhancers	Fetal Muscle Trunk	muscle
19	chr2:20775200-20780800	Enhancers	Placenta Amnion	Placenta Amnion
20	chr2:20775200-20781000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:20775400-20780000	Enhancers	Fetal Intestine Small	intestine
22	chr2:20776800-20780000	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr2:20777000-20779600	Enhancers	Primary B cells from peripheral blood	blood
24	chr2:20777000-20780000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:20777000-20780000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:20777000-20780000	Enhancers	Duodenum Mucosa	Duodenum
27	chr2:20777000-20780000	Enhancers	Right Ventricle	heart
28	chr2:20777000-20780000	Enhancers	HMEC	breast
29	chr2:20777000-20780000	Enhancers	NHEK	skin
30	chr2:20777000-20780800	Enhancers	NHLF	lung
31	chr2:20777000-20781000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:20777000-20781000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:20777000-20781000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:20777000-20781000	Enhancers	Stomach Mucosa	stomach
35	chr2:20777000-20782000	Enhancers	Brain Cingulate Gyrus	brain
36	chr2:20777200-20779400	Enhancers	NH-A	brain
37	chr2:20777200-20779800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:20777200-20780000	Enhancers	Psoas Muscle	Psoas
39	chr2:20777200-20780200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:20777200-20780200	Enhancers	NHDF-Ad	bronchial
41	chr2:20777200-20781000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr2:20777400-20780000	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr2:20777400-20780000	Enhancers	Small Intestine	intestine
44	chr2:20777400-20780000	Enhancers	Osteobl	bone
45	chr2:20777600-20779400	Enhancers	Colonic Mucosa	Colon
46	chr2:20777600-20780000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:20777600-20780000	Enhancers	Brain Angular Gyrus	brain
48	chr2:20777600-20780200	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr2:20777600-20780400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:20777600-20781000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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