Variant report

Variant	rs12617858
Chromosome Location	chr2:128026125-128026126
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:128023731..128026474-chr2:128028520..128030504,2	K562	blood:
2	chr2:128023647..128026274-chr2:128041250..128043477,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10167294	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10928764	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1143407	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11684068	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11899601	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12613252	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12613254	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12613413	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12614320	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12619391	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13017103	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13034157	0.84[EUR][1000 genomes]
rs13390029	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13403918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409933	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13414676	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13429925	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2134794	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2139142	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2276682	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2276683	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28807127	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3088374	0.87[ASN][1000 genomes]
rs34006114	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34441363	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34487399	0.92[EUR][1000 genomes]
rs34601617	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34703177	0.91[EUR][1000 genomes]
rs35708549	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3738948	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3893313	0.94[EUR][1000 genomes]
rs4150434	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150492	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150506	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150514	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4300780	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4359587	0.94[EUR][1000 genomes]
rs4528711	0.88[EUR][1000 genomes]
rs4662721	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4662724	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58063879	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59027829	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6430937	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6716392	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6735779	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6738811	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6747862	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6752139	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67771362	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7584659	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9752366	0.85[EUR][1000 genomes]
rs9923	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv1006112	chr2:127830117-128032546	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv999809	chr2:127841930-128032546	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1010669	chr2:127848860-128032546	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1003599	chr2:127871183-128059407	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv535920	chr2:127871183-128059407	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs12617858	AC068282.3	cis	Stomach	GTEx
rs12617858	AC068282.3	cis	Esophagus Mucosa	GTEx
rs12617858	AC068282.3	cis	Esophagus Muscularis	GTEx
rs12617858	AC068282.3	cis	Artery Aorta	GTEx
rs12617858	AC068282.3	cis	Skin Sun Exposed Lower leg	GTEx
rs12617858	AC068282.3	cis	Muscle Skeletal	GTEx
rs12617858	AC068282.3	cis	Adipose Subcutaneous	GTEx
rs12617858	AC068282.3	cis	lung	GTEx
rs12617858	AC068282.3	cis	Artery Tibial	GTEx
rs12617858	AC068282.3	cis	Nerve Tibial	GTEx
rs12617858	AC068282.3	cis	Thyroid	GTEx
rs12617858	AC068282.3	cis	Heart Left Ventricle	GTEx
rs12617858	AC068282.3	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128012400-128028000	Weak transcription	Hela-S3	cervix
2	chr2:128012600-128026200	Weak transcription	Stomach Mucosa	stomach
3	chr2:128013600-128036200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:128014000-128041000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:128014600-128041000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:128016200-128027800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:128017200-128027400	Weak transcription	Esophagus	oesophagus
8	chr2:128017600-128026400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:128017600-128027800	Weak transcription	Small Intestine	intestine
10	chr2:128019000-128026200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:128019000-128026200	Weak transcription	NHEK	skin
12	chr2:128019000-128027400	Weak transcription	Fetal Brain Male	brain
13	chr2:128019000-128027400	Weak transcription	Pancreas	Pancrea
14	chr2:128019000-128027600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:128019000-128028200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:128019000-128028200	Weak transcription	NHLF	lung
17	chr2:128019200-128026200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:128019400-128027800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr2:128019400-128028000	Weak transcription	K562	blood
20	chr2:128019800-128026200	Weak transcription	Fetal Heart	heart
21	chr2:128020200-128028000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr2:128021200-128050000	Strong transcription	Fetal Stomach	stomach
23	chr2:128022200-128028200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:128023200-128027200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:128023200-128036200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr2:128023200-128041000	Strong transcription	Fetal Muscle Trunk	muscle
27	chr2:128023400-128050400	Strong transcription	Liver	Liver
28	chr2:128023800-128039400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:128024000-128040800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:128024200-128032800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:128024200-128036200	Strong transcription	Placenta	Placenta
32	chr2:128024200-128036200	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr2:128024200-128038200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:128024200-128040800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr2:128024200-128050600	Strong transcription	Fetal Intestine Large	intestine
36	chr2:128024400-128027000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:128024400-128032600	Strong transcription	HSMMtube	muscle
38	chr2:128024400-128036200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr2:128024400-128038400	Strong transcription	Ovary	ovary
40	chr2:128024400-128040800	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr2:128024400-128041000	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr2:128024400-128041000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:128024400-128041000	Strong transcription	Fetal Muscle Leg	muscle
44	chr2:128024400-128049600	Strong transcription	Duodenum Mucosa	Duodenum
45	chr2:128024400-128049800	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr2:128024400-128050000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:128024400-128050200	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr2:128024400-128050200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr2:128024400-128050200	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:128024400-128050400	Strong transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links