Variant report

Variant	rs12507095
Chromosome Location	chr4:160205362-160205363
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:160203793..160205829-chr4:160213444..160214997,2	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10017696	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11100215	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12499444	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13103075	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13145422	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13150322	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28562885	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4295222	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6811571	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6816396	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6824247	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6824488	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6834008	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6835746	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847780	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6848217	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6848706	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7349689	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9990664	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830129	chr4:160061694-160270760	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv1022771	chr4:160188801-160324683	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12507095	RAPGEF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:160149400-160216800	Weak transcription	Small Intestine	intestine
2	chr4:160173200-160217400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:160186800-160225400	Weak transcription	Primary B cells from cord blood	blood
4	chr4:160189400-160235200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:160193400-160205600	Weak transcription	Right Ventricle	heart
6	chr4:160193400-160240200	Weak transcription	Gastric	stomach
7	chr4:160194200-160210000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr4:160194400-160209600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr4:160194400-160235600	Weak transcription	Fetal Stomach	stomach
10	chr4:160194400-160236600	Weak transcription	Primary T cells from cord blood	blood
11	chr4:160194600-160209400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr4:160195200-160209800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr4:160195200-160225600	Weak transcription	Placenta	Placenta
14	chr4:160200600-160235600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:160201000-160205800	Enhancers	Liver	Liver
16	chr4:160201200-160205400	Enhancers	Fetal Intestine Small	intestine
17	chr4:160201200-160205600	Weak transcription	Left Ventricle	heart
18	chr4:160201800-160217200	Weak transcription	GM12878-XiMat	blood
19	chr4:160202200-160205600	Enhancers	HepG2	liver
20	chr4:160202400-160205800	Enhancers	Fetal Intestine Large	intestine
21	chr4:160202800-160206400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:160202800-160206400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:160203000-160205400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr4:160203000-160205600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:160203000-160205600	Enhancers	Fetal Heart	heart
26	chr4:160203000-160205600	Enhancers	Osteobl	bone
27	chr4:160203000-160205800	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr4:160203000-160206200	Enhancers	HSMM	muscle
29	chr4:160203200-160205600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:160203200-160205800	Enhancers	Fetal Brain Male	brain
31	chr4:160203200-160205800	Enhancers	Fetal Kidney	kidney
32	chr4:160203200-160206400	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr4:160203400-160209600	Weak transcription	Psoas Muscle	Psoas
34	chr4:160203600-160205400	Enhancers	Hela-S3	cervix
35	chr4:160203600-160205600	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr4:160203600-160205600	Enhancers	Brain Substantia Nigra	brain
37	chr4:160203600-160205600	Enhancers	Fetal Lung	lung
38	chr4:160203600-160205800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:160203600-160205800	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr4:160203600-160216600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:160203800-160205600	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr4:160203800-160205600	Weak transcription	Pancreas	Pancrea
43	chr4:160203800-160205800	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr4:160203800-160205800	Enhancers	HUVEC	blood vessel
45	chr4:160203800-160207800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr4:160204200-160207200	Enhancers	Brain Angular Gyrus	brain
47	chr4:160204600-160205400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr4:160204600-160205400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr4:160204600-160205600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr4:160204800-160205400	Enhancers	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links