Variant report

Variant	rs13015744
Chromosome Location	chr2:55789655-55789656
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:55789601-55789731	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55783514..55785214-chr2:55789594..55791177,2	K562	blood:

Variant related genes	Relation type
ENSG00000212175	TF binding region

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1013138	0.81[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12473585	0.85[ASN][1000 genomes]
rs12473621	0.85[ASN][1000 genomes]
rs12612227	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12617627	1.00[CEU][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12618859	0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12619903	0.86[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs12620407	0.81[AMR][1000 genomes]
rs12986444	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12986587	0.83[JPT][hapmap]
rs12986797	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12991267	0.86[ASN][1000 genomes]
rs12992408	1.00[CEU][hapmap];0.83[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12993624	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12994656	0.90[CHB][hapmap]
rs12997291	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12998664	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs12998780	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12998925	0.82[AFR][1000 genomes]
rs12999506	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12999680	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12999966	0.90[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs13001425	0.81[CHB][hapmap]
rs13003270	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13004436	0.90[CHB][hapmap]
rs13005678	0.80[AFR][1000 genomes]
rs13006502	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13007577	0.80[ASN][1000 genomes]
rs13009239	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13009906	0.89[JPT][hapmap]
rs13010217	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13014123	0.83[AMR][1000 genomes]
rs13014898	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13015018	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13015030	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13018767	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13019595	0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13021958	0.93[CEU][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13025331	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13027095	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13027803	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13027853	0.94[ASN][1000 genomes]
rs13030396	0.90[CHB][hapmap]
rs13032503	0.89[JPT][hapmap]
rs1318672	0.94[CEU][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1443746	0.85[CHB][hapmap]
rs17737233	0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs17800203	0.86[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2291336	0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34013926	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34129478	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34143512	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34513671	0.83[AMR][1000 genomes]
rs35057183	0.81[ASN][1000 genomes]
rs35124901	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs35255044	0.93[ASN][1000 genomes]
rs35968359	0.97[ASN][1000 genomes]
rs3791654	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3828238	0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4312532	0.80[JPT][hapmap]
rs4322879	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs5012561	0.81[JPT][hapmap]
rs55888859	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56122729	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs66545054	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6737995	0.89[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6753530	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs6757006	0.81[JPT][hapmap]
rs8080	0.87[CEU][hapmap];0.84[JPT][hapmap];0.84[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv874160	chr2:55713102-55828974	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv525434	chr2:55716650-55841640	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13015744	SMEK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55748000-55793800	Weak transcription	Psoas Muscle	Psoas
2	chr2:55752600-55831400	Weak transcription	Stomach Mucosa	stomach
3	chr2:55769600-55816000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:55770400-55818200	Weak transcription	Small Intestine	intestine
5	chr2:55770600-55821600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr2:55770800-55815800	Strong transcription	Liver	Liver
7	chr2:55775200-55798000	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr2:55779400-55792200	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr2:55779400-55793000	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr2:55779400-55795000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:55779400-55798200	Strong transcription	Placenta	Placenta
12	chr2:55779400-55801400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr2:55779600-55793400	Strong transcription	Adipose Nuclei	Adipose
14	chr2:55779600-55797400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr2:55779600-55816200	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr2:55779600-55831400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr2:55780000-55791600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr2:55780000-55792200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr2:55780000-55792600	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:55780000-55801400	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr2:55780200-55792200	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr2:55781000-55792000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
23	chr2:55781200-55792000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr2:55781200-55794200	Strong transcription	Fetal Lung	lung
25	chr2:55781400-55791200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:55781600-55808800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:55782200-55797400	Strong transcription	Fetal Muscle Trunk	muscle
28	chr2:55783000-55789800	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr2:55783000-55791800	Strong transcription	Stomach Smooth Muscle	stomach
30	chr2:55783400-55792000	Strong transcription	Duodenum Mucosa	Duodenum
31	chr2:55783600-55791000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:55783800-55789800	Strong transcription	Spleen	Spleen
33	chr2:55783800-55790200	Strong transcription	Brain Hippocampus Middle	brain
34	chr2:55783800-55790800	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr2:55783800-55797000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:55784000-55790600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:55784000-55790800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:55784000-55792400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:55784200-55791000	Strong transcription	Left Ventricle	heart
40	chr2:55784200-55792200	Strong transcription	Fetal Intestine Large	intestine
41	chr2:55784200-55795400	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr2:55785000-55805000	Weak transcription	NHEK	skin
43	chr2:55786400-55790200	Strong transcription	Brain Cingulate Gyrus	brain
44	chr2:55786400-55792000	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr2:55786600-55791400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr2:55786600-55791400	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr2:55787400-55791800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
48	chr2:55787600-55789800	Strong transcription	Pancreas	Pancrea
49	chr2:55787600-55790200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
50	chr2:55787600-55790800	Strong transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links