Variant report

Variant	rs223408
Chromosome Location	chr4:103736345-103736346
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:103681154..103682774-chr4:103734454..103736897,2	MCF-7	breast:
2	chr4:103715909..103718007-chr4:103736247..103738557,2	MCF-7	breast:
3	chr4:103730843..103736706-chr4:103746374..103749972,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109332	Chromatin interaction
ENSG00000109323	Chromatin interaction
ENSG00000246560	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs13112128	0.80[JPT][hapmap]
rs223391	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs223495	0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs223496	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs223499	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs223500	0.89[CHD][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap]
rs223501	0.80[JPT][hapmap]
rs223504	0.80[JPT][hapmap]
rs223508	0.80[JPT][hapmap]
rs223510	0.80[JPT][hapmap]
rs227285	0.80[JPT][hapmap]
rs227369	0.80[JPT][hapmap]
rs227372	0.80[JPT][hapmap]
rs9994654	0.82[CEU][hapmap];0.89[LWK][hapmap];0.96[MKK][hapmap];0.94[YRI][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs223408	KRT8P46	cis	Esophagus Mucosa	GTEx
rs223408	MANBA	cis	multi-tissue	Pritchard
rs223408	KRT8P46	cis	lung	GTEx
rs223408	NPNT	cis	parietal	SCAN
rs223408	CISD2	cis	cerebellum	SCAN
rs223408	MANBA	cis	parietal	SCAN
rs223408	MANBA	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103712400-103737200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:103712600-103739600	Strong transcription	Fetal Thymus	thymus
3	chr4:103712800-103736800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:103713000-103744400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:103714000-103740800	Weak transcription	Aorta	Aorta
6	chr4:103714800-103737200	Strong transcription	Dnd41	blood
7	chr4:103718200-103739200	Weak transcription	Stomach Mucosa	stomach
8	chr4:103723800-103737000	Weak transcription	Colonic Mucosa	Colon
9	chr4:103724400-103745800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr4:103725000-103740600	Weak transcription	Fetal Brain Female	brain
11	chr4:103725600-103745000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr4:103726800-103738600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr4:103728400-103744400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr4:103728600-103737400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr4:103730000-103740600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
16	chr4:103730200-103737000	Weak transcription	Hela-S3	cervix
17	chr4:103730600-103737000	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr4:103731000-103736600	Genic enhancers	Primary T cells fromperipheralblood	blood
19	chr4:103731200-103736600	Strong transcription	HSMM	muscle
20	chr4:103731200-103737000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr4:103731200-103737800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr4:103731400-103736600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:103731400-103740600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:103731600-103736600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr4:103731800-103739000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr4:103732000-103737400	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr4:103732000-103737400	Strong transcription	Primary B cells from cord blood	blood
28	chr4:103732000-103739600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:103732400-103736800	Weak transcription	HSMMtube	muscle
30	chr4:103732600-103738000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr4:103732600-103744400	Weak transcription	Brain Germinal Matrix	brain
32	chr4:103732800-103736800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:103732800-103739200	Weak transcription	Fetal Muscle Leg	muscle
34	chr4:103732800-103740000	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr4:103732800-103745000	Weak transcription	Lung	lung
36	chr4:103732800-103746400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr4:103732800-103746400	Weak transcription	Esophagus	oesophagus
38	chr4:103733000-103741600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr4:103733200-103737400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr4:103733400-103736400	Strong transcription	Osteobl	bone
41	chr4:103733400-103737200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr4:103733400-103741000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr4:103733400-103743200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr4:103733600-103737200	Weak transcription	Gastric	stomach
45	chr4:103733600-103737200	Weak transcription	Thymus	Thymus
46	chr4:103733800-103737200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:103733800-103737200	Weak transcription	Ovary	ovary
48	chr4:103733800-103738400	Weak transcription	Right Ventricle	heart
49	chr4:103734000-103736800	Weak transcription	Fetal Heart	heart
50	chr4:103734000-103738200	Weak transcription	Stomach Smooth Muscle	stomach

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