Variant report

Variant	rs13010217
Chromosome Location	chr2:55806462-55806463
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55805782..55807351-chr2:55817870..55819389,2	K562	blood:
2	chr2:55760539..55763166-chr2:55804939..55807454,2	K562	blood:
3	chr2:55802486..55808781-chr2:55841275..55846052,6	MCF-7	breast:
4	chr2:55806123..55808942-chr2:55812057..55814728,2	MCF-7	breast:
5	chr2:55802504..55805545-chr2:55806244..55808758,3	K562	blood:
6	chr2:55804205..55806609-chr2:55843203..55845662,2	K562	blood:
7	chr2:55677655..55680437-chr2:55805016..55806696,2	K562	blood:

Variant related genes	Relation type
ENSG00000138041	Chromatin interaction
ENSG00000238619	Chromatin interaction
ENSG00000272606	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1013138	0.92[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12473585	0.89[ASN][1000 genomes]
rs12473621	0.89[ASN][1000 genomes]
rs12612227	0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12617627	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12618859	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12619903	0.81[CHB][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap];0.84[ASN][1000 genomes]
rs12620407	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12986444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12986587	0.83[JPT][hapmap]
rs12986797	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12987272	0.84[CHB][hapmap];0.84[CHD][hapmap]
rs12992408	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12993624	1.00[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12993839	0.84[CHD][hapmap]
rs12994656	0.84[CHB][hapmap]
rs12997291	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12998664	0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs12998780	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12999506	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12999680	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12999966	0.85[CHB][hapmap];0.83[JPT][hapmap];0.96[YRI][hapmap];0.88[ASN][1000 genomes]
rs13001425	0.92[YRI][hapmap]
rs13003270	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13004436	0.84[CHB][hapmap]
rs13005678	0.85[AFR][1000 genomes]
rs13006502	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13007577	0.82[ASN][1000 genomes]
rs13009239	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13009447	0.91[YRI][hapmap]
rs13009906	0.93[ASW][hapmap];0.89[JPT][hapmap];0.85[LWK][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs13013133	0.83[ASN][1000 genomes]
rs13013699	0.83[ASN][1000 genomes]
rs13014123	0.84[AMR][1000 genomes]
rs13014898	1.00[CEU][hapmap];0.83[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13015018	1.00[CEU][hapmap];0.89[JPT][hapmap];0.81[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13015030	1.00[CEU][hapmap];0.89[JPT][hapmap];0.81[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13015744	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]
rs13018767	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13019595	0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs13021958	0.92[CEU][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13025331	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13027095	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13027803	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13027853	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs13030396	0.84[CHB][hapmap]
rs13032503	0.93[ASW][hapmap];0.89[JPT][hapmap];0.85[LWK][hapmap];0.83[MKK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs1318672	0.94[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1443746	0.81[CHB][hapmap];1.00[CHD][hapmap]
rs17737233	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs17800203	0.80[CHB][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1822513	0.92[YRI][hapmap]
rs2291336	0.86[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.95[ASN][1000 genomes]
rs34013926	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34129478	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs34143512	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34513671	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs35124901	0.96[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs35255044	0.97[ASN][1000 genomes]
rs35968359	0.91[ASN][1000 genomes]
rs3748944	0.84[CHB][hapmap]
rs3791654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3828238	0.93[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.80[MKK][hapmap];0.95[ASN][1000 genomes]
rs4312532	0.84[JPT][hapmap]
rs4322879	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs5012561	0.89[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs55888859	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56122729	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66545054	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6737995	1.00[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6753530	0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs6757006	0.89[JPT][hapmap];0.96[YRI][hapmap]
rs7575170	0.85[ASW][hapmap];0.96[YRI][hapmap]
rs8080	0.87[CEU][hapmap];0.80[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.84[LWK][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13010217	SMEK2	cis	lymphoblastoid	seeQTL
rs13010217	SMEK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 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	chr2:55769600-55816000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:55770400-55818200	Weak transcription	Small Intestine	intestine
4	chr2:55770600-55821600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr2:55770800-55815800	Strong transcription	Liver	Liver
6	chr2:55779600-55816200	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:55779600-55831400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr2:55781600-55808800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:55788600-55816600	Strong transcription	Primary B cells from peripheral blood	blood
10	chr2:55788800-55808200	Weak transcription	Right Ventricle	heart
11	chr2:55788800-55825200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:55789800-55808200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:55789800-55822800	Weak transcription	HSMMtube	muscle
14	chr2:55789800-55843600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:55790200-55812800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr2:55790200-55829000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr2:55790200-55842400	Weak transcription	Fetal Brain Male	brain
18	chr2:55790400-55808800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:55790400-55836200	Weak transcription	Fetal Heart	heart
20	chr2:55790800-55816600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:55790800-55819400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:55791200-55812200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:55793400-55817000	Strong transcription	Fetal Thymus	thymus
24	chr2:55794200-55808000	Strong transcription	Duodenum Mucosa	Duodenum
25	chr2:55794200-55808800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr2:55794200-55818200	Weak transcription	Psoas Muscle	Psoas
27	chr2:55794400-55812200	Weak transcription	NHLF	lung
28	chr2:55794400-55825200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr2:55794400-55829000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr2:55794800-55816200	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr2:55795000-55807200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:55795400-55807800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:55795600-55806800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:55796000-55807200	Weak transcription	HMEC	breast
35	chr2:55796800-55823800	Weak transcription	Thymus	Thymus
36	chr2:55796800-55825200	Weak transcription	Brain Substantia Nigra	brain
37	chr2:55796800-55825600	Weak transcription	Pancreas	Pancrea
38	chr2:55796800-55829400	Weak transcription	Esophagus	oesophagus
39	chr2:55796800-55842600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr2:55797000-55811400	Weak transcription	Brain Germinal Matrix	brain
41	chr2:55797000-55818200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr2:55797000-55824200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:55797000-55828000	Weak transcription	Aorta	Aorta
44	chr2:55797000-55829400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr2:55797000-55829600	Weak transcription	Gastric	stomach
46	chr2:55797600-55810600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr2:55798000-55812200	Weak transcription	Brain Angular Gyrus	brain
48	chr2:55799600-55807600	Strong transcription	Fetal Intestine Large	intestine
49	chr2:55799600-55809000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:55799600-55810600	Strong transcription	Primary T helper cells fromperipheralblood	blood

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