Variant report

Variant	rs12537955
Chromosome Location	chr7:66408193-66408194
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	chr7:66384580..66387165-chr7:66405669..66409377,3	K562	blood:

Variant related genes	Relation type
ENSG00000106609	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs12531402	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs12531516	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12532147	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs12532160	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12532307	0.87[EUR][1000 genomes]
rs12532650	0.81[AMR][1000 genomes]
rs12533830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12534401	0.82[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs12535268	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12537825	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12538126	1.00[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12539366	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12539848	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs12540312	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12540447	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12540695	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17138017	1.00[CEU][hapmap]
rs17567255	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2091314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2293351	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34758320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3778906	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs3778911	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3800813	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3800819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3823608	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs4717323	0.81[AMR][1000 genomes]
rs4717324	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4717329	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4717332	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4718398	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4718426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4718434	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4718438	0.82[CHB][hapmap]
rs62465688	0.87[AMR][1000 genomes]
rs62465698	0.87[AMR][1000 genomes]
rs62465699	0.87[AMR][1000 genomes]
rs62465700	0.81[AMR][1000 genomes]
rs62465701	0.81[AMR][1000 genomes]
rs62465705	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62465706	0.87[AMR][1000 genomes]
rs62465707	0.87[AMR][1000 genomes]
rs62465709	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62465710	1.00[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs62465712	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62465713	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62465714	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62465716	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62465730	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62465734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62465736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465742	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62465752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62466575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62466578	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62466582	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62466584	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62466586	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62466588	0.87[AMR][1000 genomes]
rs62466589	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758118	chr7:66401430-66859253	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2759535	chr7:66401430-66859253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv436556	chr7:66403338-66410081	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12537955	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL
rs12537955	hmm32897	cis	multi-tissue	Pritchard
rs12537955	RABGEF1	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66387600-66409800	Weak transcription	Fetal Kidney	kidney
2	chr7:66387600-66428000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:66391200-66409800	Weak transcription	Brain Germinal Matrix	brain
4	chr7:66393400-66411800	Weak transcription	Stomach Mucosa	stomach
5	chr7:66393800-66422200	Weak transcription	Fetal Heart	heart
6	chr7:66395800-66412800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr7:66396000-66408200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr7:66396000-66409800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:66396000-66415800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr7:66398400-66410000	Weak transcription	Right Ventricle	heart
11	chr7:66398800-66409800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr7:66398800-66409800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr7:66398800-66410000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr7:66398800-66415400	Weak transcription	Brain Angular Gyrus	brain
15	chr7:66399200-66409600	Weak transcription	Aorta	Aorta
16	chr7:66400600-66426400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr7:66401800-66409400	Weak transcription	Fetal Lung	lung
18	chr7:66402000-66408200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr7:66402400-66424200	Strong transcription	Dnd41	blood
20	chr7:66402600-66414000	Strong transcription	Primary T cells from cord blood	blood
21	chr7:66403000-66424800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr7:66403200-66409800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr7:66403200-66409800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr7:66403400-66417000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr7:66403400-66417200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr7:66403400-66424400	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr7:66403400-66426000	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr7:66403400-66426400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr7:66403600-66411400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr7:66403600-66411400	Strong transcription	Duodenum Mucosa	Duodenum
31	chr7:66403600-66417200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr7:66403600-66424600	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr7:66403600-66425600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr7:66403600-66426400	Strong transcription	Thymus	Thymus
35	chr7:66403600-66426600	Strong transcription	Fetal Stomach	stomach
36	chr7:66403800-66417200	Strong transcription	Primary B cells from peripheral blood	blood
37	chr7:66403800-66418800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr7:66403800-66425200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr7:66403800-66425800	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr7:66404000-66408800	Strong transcription	Primary B cells from cord blood	blood
41	chr7:66404000-66414000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr7:66404000-66414000	Strong transcription	K562	blood
43	chr7:66404000-66417400	Strong transcription	Lung	lung
44	chr7:66405000-66424600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr7:66405200-66422800	Strong transcription	Fetal Muscle Leg	muscle
46	chr7:66405400-66408800	Strong transcription	HMEC	breast
47	chr7:66405400-66409800	Strong transcription	Fetal Intestine Small	intestine
48	chr7:66405400-66410600	Strong transcription	Primary hematopoietic stem cells	blood
49	chr7:66405400-66412800	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr7:66405400-66417400	Strong transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links