Variant report

Variant	rs10496047
Chromosome Location	chr2:55841033-55841034
allele	C/T
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	chr2:55840104-55841386	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55645913..55647717-chr2:55840630..55843041,2	K562	blood:
2	chr12:96894523..96895371-chr2:55840752..55841281,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272606	TF binding region
ENSG00000115355	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10496043	1.00[ASW][hapmap];0.92[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12470253	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12471135	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12472098	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12476169	1.00[ASN][1000 genomes]
rs1454426	0.80[EUR][1000 genomes]
rs1579780	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17278148	1.00[ASN][1000 genomes]
rs17278197	1.00[ASN][1000 genomes]
rs17369240	1.00[ASN][1000 genomes]
rs17737937	0.92[CEU][hapmap];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17792798	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17792822	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17800851	0.92[CEU][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs41281507	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4671247	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4671251	1.00[ASN][1000 genomes]
rs4671256	1.00[ASN][1000 genomes]
rs4672053	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4672057	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4672059	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4672060	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4672062	1.00[ASN][1000 genomes]
rs4672064	1.00[ASN][1000 genomes]
rs55635545	1.00[ASN][1000 genomes]
rs55850643	0.80[EUR][1000 genomes]
rs55919620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55987004	0.81[EUR][1000 genomes]
rs56071955	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56227318	0.86[EUR][1000 genomes]
rs56286204	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56299972	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56769899	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60312537	0.80[EUR][1000 genomes]
rs6729021	1.00[ASN][1000 genomes]
rs6741902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6752098	0.80[EUR][1000 genomes]
rs72812189	1.00[ASN][1000 genomes]
rs72812199	1.00[ASN][1000 genomes]
rs72814203	1.00[ASN][1000 genomes]
rs72814204	1.00[ASN][1000 genomes]
rs72814206	1.00[ASN][1000 genomes]
rs72814216	1.00[ASN][1000 genomes]
rs72814217	1.00[ASN][1000 genomes]
rs72814219	1.00[ASN][1000 genomes]
rs72814230	1.00[ASN][1000 genomes]
rs72814233	1.00[ASN][1000 genomes]
rs72814235	1.00[ASN][1000 genomes]
rs72814236	1.00[ASN][1000 genomes]
rs72814242	1.00[ASN][1000 genomes]
rs73940304	1.00[ASN][1000 genomes]
rs7568378	1.00[ASN][1000 genomes]
rs7569732	1.00[ASN][1000 genomes]
rs7584017	1.00[ASN][1000 genomes]
rs7586423	1.00[ASN][1000 genomes]
rs7600034	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs7603050	1.00[ASN][1000 genomes]

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
rs10496047	SMEK2	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55789800-55843600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55790200-55842400	Weak transcription	Fetal Brain Male	brain
3	chr2:55796800-55842600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:55826000-55841600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:55826200-55842600	Weak transcription	Right Ventricle	heart
6	chr2:55826200-55843000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:55828200-55843600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:55829800-55842800	Weak transcription	Colonic Mucosa	Colon
9	chr2:55830400-55842800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:55830400-55843600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:55830400-55843600	Weak transcription	Aorta	Aorta
12	chr2:55832400-55842800	Weak transcription	Lung	lung
13	chr2:55835400-55842800	Weak transcription	Gastric	stomach
14	chr2:55836000-55842600	Weak transcription	Psoas Muscle	Psoas
15	chr2:55836000-55842600	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr2:55836600-55843600	Weak transcription	Small Intestine	intestine
17	chr2:55836800-55842600	Weak transcription	Right Atrium	heart
18	chr2:55836800-55842800	Weak transcription	Left Ventricle	heart
19	chr2:55836800-55843600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:55837000-55842400	Weak transcription	Fetal Heart	heart
21	chr2:55837400-55841600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:55837400-55842000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:55837400-55842600	Strong transcription	Primary B cells from peripheral blood	blood
24	chr2:55837400-55842600	Strong transcription	Fetal Thymus	thymus
25	chr2:55837600-55842000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:55837600-55842200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:55837600-55842400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:55837600-55842400	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr2:55837600-55842400	Strong transcription	HSMM	muscle
30	chr2:55837800-55841400	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:55837800-55841600	Weak transcription	Fetal Kidney	kidney
32	chr2:55837800-55842000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:55837800-55842200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:55837800-55842400	Strong transcription	Placenta	Placenta
35	chr2:55837800-55842400	Strong transcription	Osteobl	bone
36	chr2:55837800-55842600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr2:55837800-55843400	Weak transcription	Stomach Mucosa	stomach
38	chr2:55838000-55841600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr2:55838000-55841600	Strong transcription	HUVEC	blood vessel
40	chr2:55838000-55842200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr2:55838000-55842200	Strong transcription	Adipose Nuclei	Adipose
42	chr2:55838000-55842400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:55838000-55842600	Strong transcription	Brain Germinal Matrix	brain
44	chr2:55838000-55843000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr2:55838200-55841600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr2:55838200-55841600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr2:55838200-55842200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:55838200-55842200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr2:55838200-55842600	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr2:55838200-55842600	Strong transcription	HUES64 Cell Line	embryonic stem cell

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