Variant report

Variant	rs4666430
Chromosome Location	chr2:20778459-20778460
allele	A/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:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 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	chr2:20777215..20779034-chr2:20785628..20788357,2	MCF-7	breast:
6	chr2:20100218..20102448-chr2:20777945..20780505,2	K562	blood:
7	chr2:20777789..20780759-chr2:20800338..20803588,3	K562	blood:
8	chr2:20646828..20648373-chr2:20777699..20779785,2	MCF-7	breast:
9	chr2:20644778..20652349-chr2:20775724..20782509,25	MCF-7	breast:
10	chr2:20777746..20779286-chr2:20815507..20817735,2	MCF-7	breast:
11	chr2:20741617..20743172-chr2:20777159..20778971,2	MCF-7	breast:
12	chr2:20775386..20780947-chr2:20790998..20795393,7	K562	blood:
13	chr2:20551002..20552911-chr2:20777358..20778948,2	K562	blood:
14	chr2:20777677..20780481-chr2:20791638..20794768,3	MCF-7	breast:
15	chr2:20524878..20527369-chr2:20777130..20779274,2	K562	blood:
16	chr2:20761404..20763660-chr2:20776835..20779050,2	K562	blood:
17	chr2:20777436..20779851-chr2:20800410..20803316,2	K562	blood:
18	chr2:20768883..20770506-chr2:20776488..20778619,2	MCF-7	breast:
19	chr2:20694461..20697342-chr2:20777535..20779162,2	MCF-7	breast:
20	chr2:20778242..20781356-chr2:20782083..20785108,5	MCF-7	breast:
21	chr2:20776319..20778530-chr2:20816686..20818367,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000269976	Chromatin interaction
ENSG00000228950	Chromatin interaction
ENSG00000231948	Chromatin interaction
ENSG00000055917	Chromatin interaction
ENSG00000143878	Chromatin interaction
ENSG00000183891	Chromatin interaction
ENSG00000271991	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

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	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs10190705	0.86[ASN][1000 genomes]
rs10195324	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10195722	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10200207	0.85[ASN][1000 genomes]
rs11096676	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[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	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12472478	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]
rs12621527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13013281	0.86[CHB][hapmap]
rs13031724	0.86[CHB][hapmap]
rs13032956	0.82[JPT][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	0.83[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	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4666427	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4666428	0.88[EUR][1000 genomes]
rs4666429	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4666431	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666436	0.86[CHB][hapmap]
rs56129345	0.84[ASN][1000 genomes]
rs6715159	0.86[CHB][hapmap];0.82[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes]
rs6722960	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs72782365	0.83[ASN][1000 genomes]
rs766474	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs921599	0.81[CEU][hapmap];0.86[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4666430		cis	Lymphoblastoid	GTEx

Chromatin state (count:93 , 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	chr2:20767800-20778600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr2:20767800-20782600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:20769400-20780000	Enhancers	Fetal Intestine Large	intestine
9	chr2:20769800-20781000	Enhancers	Fetal Muscle Leg	muscle
10	chr2:20772600-20781000	Enhancers	Placenta	Placenta
11	chr2:20772600-20785800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:20772800-20779400	Weak transcription	Liver	Liver
13	chr2:20772800-20780800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:20773000-20781000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:20773400-20781200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr2:20773600-20780000	Enhancers	Spleen	Spleen
17	chr2:20773600-20780200	Enhancers	Fetal Heart	heart
18	chr2:20773600-20781000	Enhancers	Lung	lung
19	chr2:20774600-20781000	Enhancers	Fetal Muscle Trunk	muscle
20	chr2:20775000-20778800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:20775200-20778800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:20775200-20780800	Enhancers	Placenta Amnion	Placenta Amnion
23	chr2:20775200-20781000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:20775400-20780000	Enhancers	Fetal Intestine Small	intestine
25	chr2:20775800-20778600	Enhancers	K562	blood
26	chr2:20776800-20779000	Enhancers	Primary B cells from cord blood	blood
27	chr2:20776800-20780000	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr2:20777000-20778600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr2:20777000-20779000	Enhancers	Gastric	stomach
30	chr2:20777000-20779600	Enhancers	Primary B cells from peripheral blood	blood
31	chr2:20777000-20780000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:20777000-20780000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:20777000-20780000	Enhancers	Duodenum Mucosa	Duodenum
34	chr2:20777000-20780000	Enhancers	Right Ventricle	heart
35	chr2:20777000-20780000	Enhancers	HMEC	breast
36	chr2:20777000-20780000	Enhancers	NHEK	skin
37	chr2:20777000-20780800	Enhancers	NHLF	lung
38	chr2:20777000-20781000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:20777000-20781000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:20777000-20781000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:20777000-20781000	Enhancers	Stomach Mucosa	stomach
42	chr2:20777000-20782000	Enhancers	Brain Cingulate Gyrus	brain
43	chr2:20777200-20778800	Enhancers	Brain Hippocampus Middle	brain
44	chr2:20777200-20779200	Enhancers	Esophagus	oesophagus
45	chr2:20777200-20779400	Enhancers	NH-A	brain
46	chr2:20777200-20779800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:20777200-20780000	Enhancers	Psoas Muscle	Psoas
48	chr2:20777200-20780200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr2:20777200-20780200	Enhancers	NHDF-Ad	bronchial
50	chr2:20777200-20781000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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