Variant report

Variant	rs223401
Chromosome Location	chr4:103738972-103738973
allele	C/T
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	POLR2A	chr4:103738021-103740122	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:103738919-103739018	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr4:103738822-103738983	GM12891	blood:	n/a	n/a
4	POLR2A	chr4:103738852-103739035	K562	blood:	n/a	n/a
5	MAFK	chr4:103738937-103739091	HepG2	liver:	n/a	chr4:103739011-103739022 chr4:103739012-103739023 chr4:103739012-103739023 chr4:103739010-103739024 chr4:103739011-103739022
6	POLR2A	chr4:103738514-103740087	HepG2	liver:	n/a	n/a
7	POLR2A	chr4:103736624-103740163	K562	blood:	n/a	n/a
8	POLR2A	chr4:103738958-103739191	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:103719443..103722708-chr4:103736970..103739381,3	K562	blood:
2	chr4:103736995..103756245-chr4:103778393..103800311,117	K562	blood:
3	chr4:103736438..103740967-chr4:103789693..103792681,4	K562	blood:

Variant related genes	Relation type
UBE2D3	TF binding region
ENSG00000238948	Chromatin interaction
ENSG00000109332	Chromatin interaction
ENSG00000145354	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10003326	0.83[JPT][hapmap]
rs10006474	0.81[CEU][hapmap]
rs10012413	0.91[JPT][hapmap]
rs10015289	0.83[JPT][hapmap]
rs11097796	0.83[JPT][hapmap]
rs11722779	0.83[JPT][hapmap]
rs11731885	0.83[JPT][hapmap]
rs11737544	0.83[JPT][hapmap]
rs12500379	0.83[JPT][hapmap]
rs12508069	0.83[JPT][hapmap]
rs13150426	0.91[JPT][hapmap]
rs1383733	0.83[JPT][hapmap]
rs150893	0.91[JPT][hapmap]
rs150895	0.91[JPT][hapmap]
rs17033381	0.83[JPT][hapmap]
rs223308	0.91[JPT][hapmap]
rs223313	0.80[JPT][hapmap]
rs223315	0.91[JPT][hapmap]
rs223317	0.87[CEU][hapmap]
rs223318	0.95[JPT][hapmap]
rs223324	0.91[JPT][hapmap]
rs223326	0.91[JPT][hapmap]
rs223330	0.91[JPT][hapmap]
rs223331	0.87[CEU][hapmap]
rs223334	0.91[JPT][hapmap]
rs223338	0.95[JPT][hapmap]
rs223339	0.91[JPT][hapmap]
rs223346	0.91[JPT][hapmap]
rs223347	0.91[JPT][hapmap]
rs223349	0.91[JPT][hapmap]
rs223350	0.87[JPT][hapmap]
rs223353	0.91[JPT][hapmap]
rs223356	0.91[JPT][hapmap]
rs223358	0.95[JPT][hapmap]
rs223359	0.91[JPT][hapmap]
rs223361	0.87[CEU][hapmap]
rs223363	0.91[JPT][hapmap]
rs223367	0.91[JPT][hapmap]
rs223374	0.87[CEU][hapmap];0.83[JPT][hapmap]
rs223383	0.81[JPT][hapmap]
rs223385	0.95[JPT][hapmap]
rs223390	0.91[JPT][hapmap]
rs223392	0.95[JPT][hapmap]
rs223395	0.86[JPT][hapmap]
rs223397	0.91[JPT][hapmap]
rs223400	0.91[JPT][hapmap]
rs223410	0.91[JPT][hapmap]
rs223412	0.91[JPT][hapmap]
rs223413	0.86[CEU][hapmap];0.82[JPT][hapmap]
rs223418	0.85[JPT][hapmap]
rs223419	0.91[JPT][hapmap]
rs223420	0.91[JPT][hapmap]
rs223425	0.91[JPT][hapmap]
rs223438	0.91[JPT][hapmap]
rs223441	0.91[JPT][hapmap]
rs223446	0.91[JPT][hapmap]
rs223447	0.91[JPT][hapmap]
rs223448	0.91[JPT][hapmap]
rs223450	0.91[JPT][hapmap]
rs223452	0.91[JPT][hapmap]
rs223454	0.91[JPT][hapmap]
rs223457	0.91[JPT][hapmap]
rs223458	0.86[JPT][hapmap]
rs223461	0.90[JPT][hapmap]
rs223467	0.91[JPT][hapmap]
rs223471	0.87[CEU][hapmap];0.83[JPT][hapmap]
rs223474	0.91[JPT][hapmap]
rs223475	0.91[JPT][hapmap]
rs223484	0.91[JPT][hapmap]
rs223486	0.91[JPT][hapmap]
rs223489	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs223490	0.82[JPT][hapmap]
rs223497	0.81[JPT][hapmap]
rs28445579	0.83[JPT][hapmap]
rs2866416	0.83[CEU][hapmap]
rs2866417	0.87[JPT][hapmap]
rs3774987	0.91[JPT][hapmap]
rs3886723	0.83[JPT][hapmap]
rs3974485	0.83[JPT][hapmap]
rs3974604	0.83[JPT][hapmap]
rs3974608	0.81[JPT][hapmap]
rs4623004	0.83[JPT][hapmap]
rs4698874	0.83[JPT][hapmap]
rs5028609	0.83[JPT][hapmap]
rs6419160	0.82[JPT][hapmap]
rs6533041	0.83[JPT][hapmap]
rs6533050	0.83[JPT][hapmap]
rs6533051	0.83[JPT][hapmap]
rs6533052	0.83[JPT][hapmap]
rs65671	0.91[JPT][hapmap]
rs6810668	0.83[JPT][hapmap]
rs6823625	0.81[JPT][hapmap]
rs6824070	0.83[JPT][hapmap]
rs6843738	0.81[CEU][hapmap]
rs6846762	0.91[JPT][hapmap]
rs6852141	0.83[JPT][hapmap]
rs6853193	0.82[JPT][hapmap]
rs724447	0.83[JPT][hapmap]
rs7254	0.95[JPT][hapmap]
rs7663876	0.83[JPT][hapmap]
rs7665026	0.81[CEU][hapmap]
rs7672319	0.83[JPT][hapmap]
rs7676765	0.83[JPT][hapmap]
rs7698608	0.83[JPT][hapmap]
rs9307281	0.83[JPT][hapmap]
rs9999303	0.83[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594957	chr4:103728010-103870091	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs223401	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs223401	MANBA	cis	multi-tissue	Pritchard
rs223401	LRRC37A15P	cis	Thyroid	GTEx
rs223401	KRT8P46	cis	lung	GTEx
rs223401	MANBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103712600-103739600	Strong transcription	Fetal Thymus	thymus
2	chr4:103713000-103744400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:103714000-103740800	Weak transcription	Aorta	Aorta
4	chr4:103718200-103739200	Weak transcription	Stomach Mucosa	stomach
5	chr4:103724400-103745800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr4:103725000-103740600	Weak transcription	Fetal Brain Female	brain
7	chr4:103725600-103745000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:103728400-103744400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr4:103730000-103740600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
10	chr4:103731400-103740600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:103731800-103739000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:103732000-103739600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr4:103732600-103744400	Weak transcription	Brain Germinal Matrix	brain
14	chr4:103732800-103739200	Weak transcription	Fetal Muscle Leg	muscle
15	chr4:103732800-103740000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr4:103732800-103745000	Weak transcription	Lung	lung
17	chr4:103732800-103746400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:103732800-103746400	Weak transcription	Esophagus	oesophagus
19	chr4:103733000-103741600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr4:103733400-103741000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr4:103733400-103743200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr4:103734600-103745600	Weak transcription	Fetal Stomach	stomach
23	chr4:103734800-103744800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr4:103735400-103739600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr4:103735400-103740800	Weak transcription	Fetal Kidney	kidney
26	chr4:103735600-103746200	Genic enhancers	Primary B cells from peripheral blood	blood
27	chr4:103735800-103739200	Strong transcription	Primary hematopoietic stem cells	blood
28	chr4:103735800-103740800	Genic enhancers	NHDF-Ad	bronchial
29	chr4:103735800-103741800	Enhancers	Small Intestine	intestine
30	chr4:103736000-103739000	Weak transcription	Left Ventricle	heart
31	chr4:103736000-103739200	Enhancers	Liver	Liver
32	chr4:103736000-103746600	Weak transcription	Pancreas	Pancrea
33	chr4:103736400-103739200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:103736400-103739600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:103736400-103740200	Enhancers	Brain Substantia Nigra	brain
36	chr4:103736600-103739200	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr4:103736600-103739200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr4:103736600-103739200	Weak transcription	Fetal Intestine Small	intestine
39	chr4:103736600-103739400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr4:103736600-103740600	Genic enhancers	Duodenum Mucosa	Duodenum
41	chr4:103736600-103742200	Enhancers	Brain Angular Gyrus	brain
42	chr4:103736600-103744400	Genic enhancers	HSMM	muscle
43	chr4:103736800-103739000	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr4:103736800-103739400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:103736800-103741000	Genic enhancers	HUVEC	blood vessel
46	chr4:103736800-103743600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
47	chr4:103737000-103739200	Strong transcription	Fetal Intestine Large	intestine
48	chr4:103737000-103739400	Enhancers	Rectal Smooth Muscle	rectum
49	chr4:103737000-103739400	Flanking Active TSS	HMEC	breast
50	chr4:103737000-103739600	Strong transcription	HUES6 Cell Line	embryonic stem cell

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