Variant report

Variant	rs4414820
Chromosome Location	chr3:111448422-111448423
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr3:111448371-111448659	Hela-S3	cervix:	n/a	n/a
2	NFIC	chr3:111448158-111448890	SK-N-SH	brain:	n/a	n/a
3	MAX	chr3:111448214-111448840	HCT-116	colon:	n/a	n/a
4	TCF12	chr3:111448198-111448947	SK-N-SH	brain:	n/a	n/a
5	MAX	chr3:111448300-111448660	HCT-116	colon:	n/a	n/a
6	GATA3	chr3:111448169-111448866	SK-N-SH	brain:	n/a	n/a
7	MYC	chr3:111448350-111448660	MCF10A-Er-Src	breast:	n/a	n/a
8	RCOR1	chr3:111448409-111448647	Hela-S3	cervix:	n/a	n/a
9	TCF7L2	chr3:111448396-111448661	Hela-S3	cervix:	n/a	n/a
10	SIN3AK20	chr3:111448398-111448677	PFSK-1	brain:	n/a	n/a
11	MYC	chr3:111448328-111448659	MCF10A-Er-Src	breast:	n/a	n/a
12	REST	chr3:111448272-111448713	PFSK-1	brain:	n/a	n/a
13	TCF12	chr3:111448203-111448914	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111448045..111449995-chr3:111576976..111579247,2	MCF-7	breast:

Variant related genes	Relation type
PLCXD2	TF binding region
PHLDB2	TF binding region
ENSG00000144824	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1105448	0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12494734	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13061461	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13083322	0.82[JPT][hapmap]
rs13086018	0.82[JPT][hapmap]
rs1398751	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1398753	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1398754	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16858448	0.82[JPT][hapmap]
rs2292518	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2399394	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3922706	0.82[CEU][hapmap]
rs3922707	0.82[CEU][hapmap]
rs3922780	0.82[CEU][hapmap]
rs4075549	0.82[CEU][hapmap]
rs4401340	0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4542994	0.82[CEU][hapmap]
rs4682298	0.86[JPT][hapmap]
rs6438012	0.82[CEU][hapmap]
rs7624162	0.90[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7627909	0.80[CEU][hapmap]
rs7646161	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7646453	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs882591	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs938219	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9854875	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9871034	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591290	chr3:111427455-111462570	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111415200-111454200	Weak transcription	Small Intestine	intestine
2	chr3:111420400-111450600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:111427600-111456000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:111428800-111451200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:111431600-111451400	Weak transcription	Gastric	stomach
6	chr3:111432000-111448600	Weak transcription	Brain Germinal Matrix	brain
7	chr3:111434000-111451200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:111440800-111451200	Weak transcription	Primary B cells from cord blood	blood
9	chr3:111441400-111451000	Weak transcription	Fetal Intestine Small	intestine
10	chr3:111441600-111449800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:111441600-111452800	Weak transcription	Placenta	Placenta
12	chr3:111442000-111450000	Weak transcription	Thymus	Thymus
13	chr3:111442000-111452000	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr3:111442000-111454200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr3:111442400-111456000	Weak transcription	Lung	lung
16	chr3:111442600-111451200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:111442800-111455800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:111443200-111454800	Weak transcription	Primary T cells from cord blood	blood
19	chr3:111443800-111451400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:111444200-111456000	Weak transcription	Aorta	Aorta
21	chr3:111444800-111449200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:111445200-111456800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:111446800-111448600	Weak transcription	Colon Smooth Muscle	Colon
24	chr3:111446800-111450200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:111447000-111449600	Enhancers	NH-A	brain
26	chr3:111447200-111449400	Enhancers	NHEK	skin
27	chr3:111447200-111451200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:111447200-111451800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:111447400-111449600	Enhancers	HSMM	muscle
30	chr3:111447400-111450200	Enhancers	HMEC	breast
31	chr3:111447400-111451000	Weak transcription	Fetal Intestine Large	intestine
32	chr3:111447600-111450000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr3:111447600-111451000	Weak transcription	Stomach Mucosa	stomach
34	chr3:111447800-111449000	Enhancers	HUVEC	blood vessel
35	chr3:111447800-111451200	Weak transcription	Duodenum Mucosa	Duodenum
36	chr3:111448000-111448600	Enhancers	HSMMtube	muscle
37	chr3:111448000-111449000	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr3:111448000-111449600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:111448000-111449600	Enhancers	Muscle Satellite Cultured Cells	--
40	chr3:111448000-111449600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:111448000-111449600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:111448000-111449600	Enhancers	Hela-S3	cervix
43	chr3:111448000-111449600	Enhancers	Osteobl	bone
44	chr3:111448000-111449800	Enhancers	NHDF-Ad	bronchial
45	chr3:111448200-111448600	Flanking Active TSS	HepG2	liver
46	chr3:111448200-111448800	Enhancers	Adipose Nuclei	Adipose
47	chr3:111448200-111448800	Enhancers	Stomach Smooth Muscle	stomach
48	chr3:111448200-111449400	Enhancers	Brain Hippocampus Middle	brain
49	chr3:111448200-111449600	Enhancers	NHLF	lung
50	chr3:111448400-111448600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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