Variant report

Variant	rs12643490
Chromosome Location	chr4:152213916-152213917
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10006188	0.96[ASN][1000 genomes]
rs10032413	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12509608	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13134038	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13134365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1875308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280280	0.83[CHB][hapmap]
rs2280283	1.00[CEU][hapmap]
rs2407165	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2407167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs2407168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736502	1.00[CEU][hapmap]
rs4504229	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4529031	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6535764	1.00[CEU][hapmap]
rs6535778	0.82[AFR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6535784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835206	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6845400	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6850311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7654306	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7656771	1.00[CEU][hapmap]
rs7668541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7691584	0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1025192	chr4:152202627-152498890	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv537307	chr4:152202627-152498890	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152196000-152218400	Weak transcription	Psoas Muscle	Psoas
2	chr4:152197800-152242400	Weak transcription	Aorta	Aorta
3	chr4:152198800-152221800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:152198800-152242800	Weak transcription	Fetal Lung	lung
5	chr4:152201600-152228600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:152202600-152214800	Weak transcription	Small Intestine	intestine
7	chr4:152203600-152215600	Weak transcription	Lung	lung
8	chr4:152203600-152216000	Weak transcription	Left Ventricle	heart
9	chr4:152203600-152243000	Weak transcription	Esophagus	oesophagus
10	chr4:152204400-152215600	Weak transcription	Right Atrium	heart
11	chr4:152205400-152216000	Weak transcription	Fetal Intestine Large	intestine
12	chr4:152206200-152215000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr4:152206200-152215000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr4:152206200-152216000	Weak transcription	Ovary	ovary
15	chr4:152206400-152215600	Weak transcription	Liver	Liver
16	chr4:152206400-152215600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr4:152206400-152216200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:152206400-152225600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr4:152206600-152216600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr4:152206800-152225400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr4:152208400-152228400	Weak transcription	Fetal Stomach	stomach
22	chr4:152209400-152217400	Weak transcription	A549	lung
23	chr4:152209600-152214600	Weak transcription	Brain Hippocampus Middle	brain
24	chr4:152211000-152214800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr4:152211200-152215000	Weak transcription	Fetal Heart	heart
26	chr4:152211200-152217400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr4:152211400-152214800	Weak transcription	Brain Angular Gyrus	brain
28	chr4:152211400-152216000	Weak transcription	Fetal Intestine Small	intestine
29	chr4:152212200-152214000	Enhancers	HUVEC	blood vessel
30	chr4:152212400-152215400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr4:152212600-152214600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr4:152212600-152215400	Weak transcription	HepG2	liver
33	chr4:152212600-152215600	Weak transcription	Right Ventricle	heart
34	chr4:152212800-152225400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:152213000-152234800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr4:152213400-152214600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr4:152213400-152218400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr4:152213400-152223200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr4:152213400-152224800	Weak transcription	HMEC	breast
40	chr4:152213400-152225600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:152213400-152228400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:152213400-152235800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr4:152213600-152215600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr4:152213600-152215600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr4:152213600-152221800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr4:152213800-152216200	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links