Variant report

Variant	rs4666429
Chromosome Location	chr2:20777617-20777618
allele	C/T
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20777398..20780363-chr2:20792130..20794608,2	MCF-7	breast:
2	chr2:20777247..20781087-chr2:20782458..20786081,5	K562	blood:
3	chr2:20664924..20667934-chr2:20777556..20780555,3	MCF-7	breast:
4	chr2:20777215..20779034-chr2:20785628..20788357,2	MCF-7	breast:
5	chr2:20644778..20652349-chr2:20775724..20782509,25	MCF-7	breast:
6	chr2:20741617..20743172-chr2:20777159..20778971,2	MCF-7	breast:
7	chr2:20775386..20780947-chr2:20790998..20795393,7	K562	blood:
8	chr2:20551002..20552911-chr2:20777358..20778948,2	K562	blood:
9	chr2:20771832..20774645-chr2:20774771..20777739,3	K562	blood:
10	chr2:20524878..20527369-chr2:20777130..20779274,2	K562	blood:
11	chr2:20761404..20763660-chr2:20776835..20779050,2	K562	blood:
12	chr2:20777436..20779851-chr2:20800410..20803316,2	K562	blood:
13	chr2:20768883..20770506-chr2:20776488..20778619,2	MCF-7	breast:
14	chr2:20694461..20697342-chr2:20777535..20779162,2	MCF-7	breast:
15	chr2:20776319..20778530-chr2:20816686..20818367,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000231948	Chromatin interaction
ENSG00000228950	Chromatin interaction
ENSG00000055917	Chromatin interaction
ENSG00000269976	Chromatin interaction
ENSG00000143878	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	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10177787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[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];1.00[ASN][1000 genomes]
rs10177834	0.82[JPT][hapmap]
rs10190705	0.96[ASN][1000 genomes]
rs10195324	1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10195722	0.83[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10200207	0.95[ASN][1000 genomes]
rs11096676	0.85[ASN][1000 genomes]
rs11096677	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1123781	0.99[ASN][1000 genomes]
rs11691255	0.96[ASN][1000 genomes]
rs11897611	0.90[ASN][1000 genomes]
rs12472478	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12621527	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13032956	0.82[JPT][hapmap]
rs13422371	0.96[ASN][1000 genomes]
rs16987857	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16987878	0.90[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs16987880	0.89[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs16987884	0.91[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs2882035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2882036	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4666315	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666426	0.85[ASN][1000 genomes]
rs4666427	0.85[ASN][1000 genomes]
rs4666430	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4666431	0.83[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs55835545	0.88[ASN][1000 genomes]
rs56129345	0.94[ASN][1000 genomes]
rs59169527	0.83[ASN][1000 genomes]
rs6715159	0.82[JPT][hapmap]
rs6722960	0.82[JPT][hapmap]
rs72782365	0.93[ASN][1000 genomes]
rs72782367	0.86[ASN][1000 genomes]
rs72782368	0.88[ASN][1000 genomes]
rs766474	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs921599	0.82[JPT][hapmap]
rs921601	0.88[ASN][1000 genomes]
rs921602	0.91[CHB][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:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20764400-20778200	Enhancers	HepG2	liver
2	chr2:20765600-20780800	Enhancers	Adipose Nuclei	Adipose
3	chr2:20765800-20786200	Enhancers	HUVEC	blood vessel
4	chr2:20766800-20780800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr2:20766800-20781000	Enhancers	Left Ventricle	heart
6	chr2:20767000-20781000	Enhancers	Right Atrium	heart
7	chr2:20767400-20778200	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr2:20767800-20778600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr2:20767800-20782600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:20769400-20780000	Enhancers	Fetal Intestine Large	intestine
11	chr2:20769800-20781000	Enhancers	Fetal Muscle Leg	muscle
12	chr2:20772600-20781000	Enhancers	Placenta	Placenta
13	chr2:20772600-20785800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:20772800-20779400	Weak transcription	Liver	Liver
15	chr2:20772800-20780800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:20773000-20777800	Weak transcription	Pancreas	Pancrea
17	chr2:20773000-20781000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:20773400-20781200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr2:20773600-20780000	Enhancers	Spleen	Spleen
20	chr2:20773600-20780200	Enhancers	Fetal Heart	heart
21	chr2:20773600-20781000	Enhancers	Lung	lung
22	chr2:20774000-20777800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:20774000-20777800	Weak transcription	HSMM	muscle
24	chr2:20774000-20778400	Weak transcription	Fetal Kidney	kidney
25	chr2:20774400-20778400	Weak transcription	HSMMtube	muscle
26	chr2:20774600-20781000	Enhancers	Fetal Muscle Trunk	muscle
27	chr2:20774800-20777800	Weak transcription	Brain Anterior Caudate	brain
28	chr2:20775000-20778800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:20775200-20778800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:20775200-20780800	Enhancers	Placenta Amnion	Placenta Amnion
31	chr2:20775200-20781000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:20775400-20777800	Weak transcription	Colon Smooth Muscle	Colon
33	chr2:20775400-20778000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr2:20775400-20780000	Enhancers	Fetal Intestine Small	intestine
35	chr2:20775600-20777800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:20775600-20777800	Weak transcription	Ovary	ovary
37	chr2:20775600-20778000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:20775600-20778400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:20775800-20778600	Enhancers	K562	blood
40	chr2:20776400-20778400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:20776600-20777800	Weak transcription	Primary hematopoietic stem cells	blood
42	chr2:20776800-20778000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr2:20776800-20779000	Enhancers	Primary B cells from cord blood	blood
44	chr2:20776800-20780000	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr2:20777000-20777800	Enhancers	GM12878-XiMat	blood
46	chr2:20777000-20778000	Weak transcription	Fetal Thymus	thymus
47	chr2:20777000-20778600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:20777000-20779000	Enhancers	Gastric	stomach
49	chr2:20777000-20779600	Enhancers	Primary B cells from peripheral blood	blood
50	chr2:20777000-20780000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links