Variant report

Variant	rs12992408
Chromosome Location	chr2:55749085-55749086
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55645285..55648583-chr2:55744780..55749543,7	K562	blood:
2	chr2:55728050..55729964-chr2:55747020..55749706,2	MCF-7	breast:
3	chr2:55747318..55749114-chr2:55750754..55752618,2	MCF-7	breast:
4	chr2:55734348..55736732-chr2:55747645..55749289,2	K562	blood:
5	chr2:55746965..55749333-chr2:55759467..55761461,2	K562	blood:

Variant related genes	Relation type
ENSG00000115355	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1013138	0.92[ASW][hapmap];0.81[CEU][hapmap];0.84[GIH][hapmap];0.88[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12612227	0.84[AFR][1000 genomes]
rs12617627	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12618859	1.00[ASW][hapmap];0.80[CHB][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.97[MKK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs12619903	0.92[YRI][hapmap]
rs12986444	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12986587	0.90[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs12986797	0.86[AFR][1000 genomes]
rs12992827	0.94[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs12993624	1.00[ASW][hapmap];0.83[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs12993642	0.82[ASN][1000 genomes]
rs12998664	0.89[JPT][hapmap]
rs12998780	0.94[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12999506	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12999680	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12999966	0.92[YRI][hapmap]
rs13001425	0.85[CHB][hapmap];0.97[CHD][hapmap];0.87[YRI][hapmap]
rs13003270	0.82[EUR][1000 genomes]
rs13005678	0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs13006502	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13009239	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13009447	0.89[CHB][hapmap];0.85[YRI][hapmap]
rs13009906	0.92[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs13010217	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]
rs13014898	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13015018	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13015030	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13015744	1.00[CEU][hapmap];0.83[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13018767	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13019595	0.84[AFR][1000 genomes]
rs13021958	0.92[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13025331	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[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]
rs13027095	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13027803	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13032503	0.92[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1318672	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17737233	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs1822513	0.90[CHB][hapmap];0.97[CHD][hapmap];0.87[YRI][hapmap]
rs2291336	0.85[ASW][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap]
rs34013926	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34143512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34679603	0.80[ASN][1000 genomes]
rs35124901	0.86[AFR][1000 genomes]
rs3791654	1.00[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap];0.93[LWK][hapmap];0.94[MKK][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3828238	0.92[ASW][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap]
rs4312532	0.89[JPT][hapmap]
rs4322879	0.83[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs5012561	0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs55888859	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs56122729	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs66545054	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6737995	1.00[ASW][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs6753530	0.89[JPT][hapmap]
rs6757006	0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7575170	0.83[ASW][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.80[JPT][hapmap];0.92[YRI][hapmap]
rs8080	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[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
rs12992408	SMEK2	cis	lymphoblastoid	seeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55747600-55752200	Weak transcription	Lung	lung
2	chr2:55747600-55753000	Weak transcription	Spleen	Spleen
3	chr2:55747800-55751000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr2:55747800-55751200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:55747800-55751400	Weak transcription	Pancreas	Pancrea
6	chr2:55747800-55752000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:55747800-55752800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:55747800-55753600	Weak transcription	Gastric	stomach
9	chr2:55747800-55784000	Weak transcription	Esophagus	oesophagus
10	chr2:55748000-55749600	Weak transcription	Fetal Stomach	stomach
11	chr2:55748000-55750000	Weak transcription	Left Ventricle	heart
12	chr2:55748000-55751400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr2:55748000-55751600	Weak transcription	Liver	Liver
14	chr2:55748000-55752000	Weak transcription	Stomach Mucosa	stomach
15	chr2:55748000-55752200	Weak transcription	Placenta	Placenta
16	chr2:55748000-55752200	Weak transcription	Ovary	ovary
17	chr2:55748000-55752200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr2:55748000-55752200	Weak transcription	Right Ventricle	heart
19	chr2:55748000-55752400	Weak transcription	Aorta	Aorta
20	chr2:55748000-55753000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr2:55748000-55757600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:55748000-55761200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr2:55748000-55761200	Weak transcription	Primary B cells from cord blood	blood
24	chr2:55748000-55784000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:55748000-55788000	Weak transcription	Colonic Mucosa	Colon
26	chr2:55748000-55793800	Weak transcription	Psoas Muscle	Psoas
27	chr2:55748200-55749400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:55748200-55749400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:55748200-55749600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:55748200-55749600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr2:55748200-55749600	Weak transcription	Fetal Intestine Small	intestine
32	chr2:55748200-55750600	Weak transcription	HUVEC	blood vessel
33	chr2:55748200-55750600	Weak transcription	NH-A	brain
34	chr2:55748200-55750800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr2:55748200-55750800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:55748200-55750800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr2:55748200-55750800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr2:55748200-55750800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr2:55748200-55750800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:55748200-55750800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr2:55748200-55750800	Weak transcription	Brain Hippocampus Middle	brain
42	chr2:55748200-55750800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr2:55748200-55750800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:55748200-55750800	Weak transcription	Fetal Thymus	thymus
45	chr2:55748200-55750800	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr2:55748200-55750800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr2:55748200-55750800	Weak transcription	HSMM	muscle
48	chr2:55748200-55750800	Weak transcription	NHDF-Ad	bronchial
49	chr2:55748200-55751000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:55748200-55751000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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