Variant report

Variant	rs223495
Chromosome Location	chr4:103656377-103656378
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	JUN	chr4:103655763-103656518	K562	blood:	n/a	chr4:103656090-103656098
2	FOXA1	chr4:103655923-103656382	HepG2	liver:	n/a	n/a
3	FOXA1	chr4:103655981-103656394	HepG2	liver:	n/a	n/a
4	FOXA1	chr4:103655979-103656439	HepG2	liver:	n/a	n/a
5	FOXA2	chr4:103655964-103656384	HepG2	liver:	n/a	n/a
6	MTA3	chr4:103655632-103656423	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:103655651..103658246-chr4:103747262..103750074,2	MCF-7	breast:
2	chr4:103651533..103654531-chr4:103655303..103657953,2	K562	blood:

Variant related genes	Relation type
LRRC37A15P	TF binding region
ENSG00000109332	Chromatin interaction
ENSG00000246560	Chromatin interaction
ENSG00000230069	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs13112128	0.93[JPT][hapmap]
rs170564	0.93[JPT][hapmap]
rs223391	1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap]
rs223408	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	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs223499	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223500	0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs223501	0.89[CEU][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap]
rs223502	1.00[ASW][hapmap];0.84[CEU][hapmap];0.93[JPT][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.96[MKK][hapmap];0.96[YRI][hapmap]
rs223504	0.93[JPT][hapmap]
rs223508	0.93[JPT][hapmap]
rs223510	0.93[JPT][hapmap]
rs227280	0.81[YRI][hapmap]
rs227283	0.88[ASW][hapmap]
rs227285	0.93[JPT][hapmap]
rs227369	0.93[JPT][hapmap]
rs227370	0.93[JPT][hapmap]
rs227372	0.93[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	nsv1008110	chr4:103560583-103684526	Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs223495	CENPE	cis	parietal	SCAN
rs223495	MANBA	cis	multi-tissue	Pritchard
rs223495	KRT8P46	cis	lung	GTEx
rs223495	NPNT	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103547000-103658200	Weak transcription	Small Intestine	intestine
2	chr4:103581800-103681000	Weak transcription	Spleen	Spleen
3	chr4:103609600-103664800	Weak transcription	Esophagus	oesophagus
4	chr4:103632400-103666200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr4:103632400-103667600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr4:103637000-103680800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr4:103638800-103681000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:103639200-103659400	Weak transcription	Ovary	ovary
9	chr4:103641000-103671600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr4:103641200-103680800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr4:103641400-103657800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr4:103641400-103659400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr4:103644600-103658200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:103644800-103658000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr4:103644800-103658000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:103645400-103657200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr4:103645400-103658200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr4:103647600-103670400	Weak transcription	Liver	Liver
19	chr4:103650200-103658200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr4:103651000-103681000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:103652000-103678800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr4:103652400-103658800	Weak transcription	Fetal Stomach	stomach
23	chr4:103652400-103665800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:103652600-103658400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr4:103652800-103663600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:103653000-103680800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr4:103653400-103656400	Enhancers	Fetal Lung	lung
28	chr4:103653600-103656800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:103653600-103673200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr4:103653800-103657800	Weak transcription	Fetal Muscle Leg	muscle
31	chr4:103654200-103656800	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr4:103654200-103658200	Weak transcription	Psoas Muscle	Psoas
33	chr4:103654600-103656400	Strong transcription	Aorta	Aorta
34	chr4:103654800-103656400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr4:103655000-103656800	Enhancers	K562	blood
36	chr4:103655200-103657000	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr4:103655200-103657200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:103655200-103658600	Enhancers	HepG2	liver
39	chr4:103655400-103656400	Enhancers	Primary T cells fromperipheralblood	blood
40	chr4:103655400-103656400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:103655400-103656400	Strong transcription	Fetal Intestine Small	intestine
42	chr4:103655400-103656400	Genic enhancers	Lung	lung
43	chr4:103655400-103656600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:103655400-103656600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr4:103655400-103656600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr4:103655400-103656600	Enhancers	Fetal Thymus	thymus
47	chr4:103655400-103656600	Genic enhancers	Gastric	stomach
48	chr4:103655400-103656600	Enhancers	Left Ventricle	heart
49	chr4:103655400-103656600	Enhancers	Right Ventricle	heart
50	chr4:103655400-103656600	Enhancers	NHDF-Ad	bronchial

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