Variant report

Variant	rs1316858
Chromosome Location	chr4:152198731-152198732
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11733600	0.82[CEU][hapmap]
rs12508449	0.82[CEU][hapmap]
rs12647331	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12649929	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13102005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13112985	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13117723	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13120319	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13126069	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13126943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13128346	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13135328	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13137979	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13148086	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13150868	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13151317	0.84[JPT][hapmap]
rs17590612	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34041707	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36097019	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3990708	0.82[CEU][hapmap]
rs3990734	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4385037	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6535785	0.81[CEU][hapmap]
rs66559303	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6819551	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6832149	0.96[CEU][hapmap];0.87[TSI][hapmap]
rs6846745	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6849871	0.82[CEU][hapmap]
rs9997353	0.96[CEU][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:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152177800-152200000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:152182600-152211000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:152182800-152206000	Weak transcription	NHEK	skin
4	chr4:152188600-152204000	Weak transcription	Gastric	stomach
5	chr4:152189400-152202400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr4:152189400-152205800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:152190800-152208600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:152191200-152204200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:152194200-152202400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:152194200-152213200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr4:152196000-152204000	Weak transcription	Fetal Stomach	stomach
12	chr4:152196000-152218400	Weak transcription	Psoas Muscle	Psoas
13	chr4:152196200-152199600	Weak transcription	Right Atrium	heart
14	chr4:152197400-152198800	Enhancers	Brain Hippocampus Middle	brain
15	chr4:152197400-152199200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr4:152197600-152198800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:152197600-152198800	Enhancers	Brain Cingulate Gyrus	brain
18	chr4:152197600-152198800	Enhancers	Brain Substantia Nigra	brain
19	chr4:152197600-152199400	Enhancers	Ovary	ovary
20	chr4:152197800-152198800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr4:152197800-152242400	Weak transcription	Aorta	Aorta
22	chr4:152198000-152202600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr4:152198200-152198800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:152198200-152198800	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr4:152198200-152198800	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr4:152198200-152198800	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr4:152198200-152198800	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr4:152198200-152198800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr4:152198200-152201400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr4:152198200-152205800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr4:152198400-152199600	Weak transcription	Left Ventricle	heart
32	chr4:152198400-152200000	Weak transcription	HepG2	liver
33	chr4:152198400-152200800	Weak transcription	Liver	Liver
34	chr4:152198400-152200800	Weak transcription	Lung	lung
35	chr4:152198400-152201800	Strong transcription	Fetal Intestine Small	intestine
36	chr4:152198600-152200000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr4:152198600-152200000	Weak transcription	Right Ventricle	heart
38	chr4:152198600-152201000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:152198600-152202000	Weak transcription	Stomach Mucosa	stomach
40	chr4:152198600-152203400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr4:152198600-152204600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr4:152198600-152204800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr4:152198600-152205000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr4:152198600-152205000	Weak transcription	Fetal Intestine Large	intestine
45	chr4:152198600-152205800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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