Variant report

Variant	rs12998664
Chromosome Location	chr2:55829585-55829586
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55827514..55830372-chr2:55836467..55838668,2	MCF-7	breast:
2	chr2:55823780..55826552-chr2:55827619..55830389,2	K562	blood:
3	chr2:55828430..55830196-chr2:55843729..55846415,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272606	Chromatin interaction
ENSG00000138041	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1013138	0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs12473585	0.88[ASN][1000 genomes]
rs12473621	0.88[ASN][1000 genomes]
rs12612227	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12617627	0.84[JPT][hapmap]
rs12618859	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12619903	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs12620407	0.83[ASN][1000 genomes]
rs12623937	0.82[AMR][1000 genomes]
rs12986444	0.94[ASN][1000 genomes]
rs12986587	0.89[JPT][hapmap]
rs12986797	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12987272	0.84[CEU][hapmap];0.84[CHD][hapmap];0.83[AMR][1000 genomes]
rs12991267	0.80[ASN][1000 genomes]
rs12992408	0.89[JPT][hapmap]
rs12992827	0.85[JPT][hapmap]
rs12993624	0.89[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs12993839	0.84[CHD][hapmap]
rs12994656	0.84[CEU][hapmap];0.90[CHB][hapmap];0.90[AMR][1000 genomes]
rs12998780	0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs12999506	0.93[ASN][1000 genomes]
rs12999966	0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs13001425	0.81[CHB][hapmap]
rs13001452	0.93[AMR][1000 genomes]
rs13004436	0.84[CEU][hapmap];0.90[CHB][hapmap];0.93[AMR][1000 genomes]
rs13005850	0.82[ASN][1000 genomes]
rs13007577	0.82[ASN][1000 genomes]
rs13007719	0.93[AMR][1000 genomes]
rs13009906	0.84[JPT][hapmap]
rs13010217	0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs13013133	0.82[ASN][1000 genomes]
rs13013699	0.82[ASN][1000 genomes]
rs13014898	0.89[JPT][hapmap]
rs13015018	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs13015030	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs13015243	0.85[AMR][1000 genomes]
rs13015744	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs13018767	0.89[ASN][1000 genomes]
rs13019595	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13025331	0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs13025994	0.90[AMR][1000 genomes]
rs13027095	0.93[ASN][1000 genomes]
rs13027803	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13027853	0.91[ASN][1000 genomes]
rs13030396	0.84[CEU][hapmap];0.90[CHB][hapmap];0.90[AMR][1000 genomes]
rs13032503	0.84[JPT][hapmap]
rs1318672	0.89[JPT][hapmap]
rs1443746	0.85[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs1542643	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs17737233	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17800203	0.85[CHB][hapmap];0.89[YRI][hapmap];0.85[ASN][1000 genomes]
rs1867334	0.81[AMR][1000 genomes]
rs2054729	0.90[AMR][1000 genomes]
rs2291336	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34129478	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34400247	0.85[AMR][1000 genomes]
rs35057183	0.90[AMR][1000 genomes]
rs35124901	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35189503	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35255044	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35861320	0.95[AMR][1000 genomes]
rs35968359	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3748944	0.84[CEU][hapmap];0.83[AMR][1000 genomes]
rs3748952	0.93[AMR][1000 genomes]
rs3791654	0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs3828238	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4322879	0.89[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs5012561	0.84[JPT][hapmap]
rs6737995	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6753530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6757006	0.84[JPT][hapmap]
rs8080	0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12998664	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	chr2:55752600-55831400	Weak transcription	Stomach Mucosa	stomach
2	chr2:55779600-55831400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr2:55789800-55843600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:55790200-55842400	Weak transcription	Fetal Brain Male	brain
5	chr2:55790400-55836200	Weak transcription	Fetal Heart	heart
6	chr2:55796800-55842600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:55797000-55829600	Weak transcription	Gastric	stomach
8	chr2:55803000-55838800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr2:55810600-55829600	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:55818600-55834400	Weak transcription	Small Intestine	intestine
11	chr2:55818600-55835200	Weak transcription	Psoas Muscle	Psoas
12	chr2:55820200-55831400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:55820400-55830400	Strong transcription	Fetal Intestine Large	intestine
14	chr2:55820600-55830600	Strong transcription	Dnd41	blood
15	chr2:55820600-55832000	Strong transcription	Primary B cells from peripheral blood	blood
16	chr2:55821400-55831200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr2:55822000-55831200	Strong transcription	Fetal Thymus	thymus
18	chr2:55822200-55830600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:55822600-55832400	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr2:55822800-55830400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:55822800-55830400	Strong transcription	Fetal Muscle Leg	muscle
22	chr2:55822800-55830400	Strong transcription	HepG2	liver
23	chr2:55822800-55830800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:55823000-55829600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:55823000-55830400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:55823000-55830600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr2:55823000-55830600	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr2:55823400-55829800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:55823600-55830400	Strong transcription	Primary hematopoietic stem cells	blood
30	chr2:55823800-55830400	Strong transcription	Fetal Intestine Small	intestine
31	chr2:55824400-55837400	Weak transcription	Fetal Kidney	kidney
32	chr2:55825200-55830600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:55825400-55830400	Strong transcription	Fetal Lung	lung
34	chr2:55826000-55831200	Weak transcription	Colon Smooth Muscle	Colon
35	chr2:55826000-55835800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:55826000-55839200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:55826000-55841600	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr2:55826200-55829600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr2:55826200-55830400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr2:55826200-55830800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr2:55826200-55831600	Weak transcription	Brain Substantia Nigra	brain
42	chr2:55826200-55836000	Weak transcription	Ovary	ovary
43	chr2:55826200-55842600	Weak transcription	Right Ventricle	heart
44	chr2:55826200-55843000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr2:55826400-55829600	Weak transcription	Brain Angular Gyrus	brain
46	chr2:55826400-55829600	Weak transcription	Thymus	Thymus
47	chr2:55827200-55830400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:55827600-55830200	Strong transcription	K562	blood
49	chr2:55827600-55831200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:55827600-55831400	Strong transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links