Variant report

Variant	rs2407167
Chromosome Location	chr4:152172980-152172981
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:152172761..152174512-chr4:152179478..152181332,2	K562	blood:
2	chr4:152172761..152174463-chr4:152179832..152182204,2	K562	blood:

Variant related genes	Relation type
ENSG00000249012	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10006188	1.00[ASN][1000 genomes]
rs10020317	0.81[GIH][hapmap]
rs10030785	0.85[GIH][hapmap]
rs10032413	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10857254	0.82[GIH][hapmap]
rs11734577	0.81[GIH][hapmap]
rs11734586	0.82[GIH][hapmap]
rs11938266	0.82[GIH][hapmap]
rs12505974	0.81[GIH][hapmap]
rs12509608	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12643490	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13134038	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13134365	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1875308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2280280	0.83[CHB][hapmap]
rs2280283	1.00[CEU][hapmap]
rs2407165	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407168	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2407220	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2407221	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2407406	0.82[GIH][hapmap]
rs2897657	0.82[GIH][hapmap]
rs3736502	1.00[CEU][hapmap]
rs4504229	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4529031	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4696229	0.82[GIH][hapmap]
rs4696235	0.82[GIH][hapmap]
rs6535764	1.00[CEU][hapmap]
rs6535778	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6535784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6835206	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6845400	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6846323	0.81[GIH][hapmap]
rs6847927	0.82[GIH][hapmap]
rs6850311	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7654306	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7656771	1.00[CEU][hapmap]
rs7659146	0.82[GIH][hapmap]
rs7668154	0.82[GIH][hapmap]
rs7668541	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7669180	0.81[GIH][hapmap]
rs7690329	0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034948	chr4:151590115-152202687	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv537302	chr4:151590115-152202687	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv530159	chr4:151624865-152203910	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152130200-152187800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr4:152149200-152185200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:152149200-152197600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr4:152149600-152173000	Weak transcription	Right Atrium	heart
5	chr4:152156000-152179800	Weak transcription	Fetal Stomach	stomach
6	chr4:152158800-152178800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:152158800-152181800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:152164800-152176800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr4:152165400-152189000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr4:152168200-152173400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr4:152169400-152176600	Weak transcription	Fetal Intestine Large	intestine
12	chr4:152169600-152176600	Weak transcription	Fetal Intestine Small	intestine
13	chr4:152170000-152173000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:152171000-152173600	Enhancers	H1 Cell Line	embryonic stem cell
15	chr4:152171000-152173800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:152171000-152175200	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr4:152171200-152173400	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr4:152171200-152173400	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr4:152171800-152174400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:152171800-152174600	Enhancers	Liver	Liver
21	chr4:152172000-152174400	Enhancers	Brain Hippocampus Middle	brain
22	chr4:152172000-152174600	Enhancers	Pancreas	Pancrea
23	chr4:152172200-152173000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:152172200-152173200	Weak transcription	Psoas Muscle	Psoas
25	chr4:152172200-152174200	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr4:152172200-152175800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr4:152172200-152178600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr4:152172200-152183400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr4:152172200-152184000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr4:152172200-152184000	Weak transcription	Lung	lung
31	chr4:152172600-152174600	Enhancers	Left Ventricle	heart
32	chr4:152172800-152173000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr4:152172800-152173200	Flanking Active TSS	HepG2	liver
34	chr4:152172800-152173400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:152172800-152173400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr4:152172800-152173400	Enhancers	Stomach Smooth Muscle	stomach
37	chr4:152172800-152174000	Enhancers	Brain Substantia Nigra	brain
38	chr4:152172800-152174000	Enhancers	Ovary	ovary
39	chr4:152172800-152174200	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr4:152172800-152174200	Enhancers	HUVEC	blood vessel
41	chr4:152172800-152190600	Weak transcription	H9 Cell Line	embryonic stem cell

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