Variant report

Variant	rs12739797
Chromosome Location	chr1:186316732-186316733
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:186314481-186317411	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:186303335..186305022-chr1:186315290..186317510,2	MCF-7	breast:
2	chr1:186314681..186317942-chr1:186341100..186345246,4	K562	blood:
3	chr1:186304225..186306669-chr1:186316291..186318175,2	K562	blood:
4	chr1:186315129..186317112-chr1:186323166..186325594,2	K562	blood:
5	chr1:186316560..186318174-chr1:186331553..186333723,2	MCF-7	breast:
6	chr1:186312933..186317180-chr1:186341100..186346147,6	K562	blood:

No data

Variant related genes	Relation type
TPR	TF binding region
ENSG00000157181	Chromatin interaction
ENSG00000047410	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11799811	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11799843	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11801527	0.91[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap]
rs11803944	0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.92[TSI][hapmap]
rs11805289	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11805302	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11806068	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11806304	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11809402	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11811320	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11812050	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs12726960	0.82[CEU][hapmap]
rs12728791	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12733799	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12740221	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12742751	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12749203	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16825403	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs1919194	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2273774	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2273775	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2293569	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2293570	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34467087	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34552348	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34924250	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35131069	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35146131	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35942197	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766698	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3766701	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3817586	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[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];0.99[ASN][1000 genomes]
rs57716405	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71634159	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1847807	chr1:186295930-186339878	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv548399	chr1:186295930-186353461	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
5	esv1822818	chr1:186301447-186441585	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv523794	chr1:186316488-186327536	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12739797	TSEN15	cis	parietal	SCAN
rs12739797	NCF2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186277600-186342600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:186278400-186342600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:186278800-186320400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:186279400-186342400	Strong transcription	Fetal Thymus	thymus
5	chr1:186279600-186317600	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr1:186279600-186342400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:186280000-186317600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:186280000-186320200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:186280000-186340400	Strong transcription	Dnd41	blood
10	chr1:186280000-186342000	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr1:186280000-186342400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:186280000-186342400	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr1:186280000-186342400	Strong transcription	Osteobl	bone
14	chr1:186280000-186342600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:186280000-186342600	Strong transcription	HSMM	muscle
16	chr1:186280200-186316800	Strong transcription	Placenta	Placenta
17	chr1:186280200-186342200	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:186280400-186317600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:186280400-186317600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:186280400-186342400	Strong transcription	Primary B cells from peripheral blood	blood
21	chr1:186280800-186342600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:186281000-186341800	Strong transcription	Liver	Liver
23	chr1:186281000-186342600	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:186281200-186317600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:186281200-186317800	Strong transcription	HUVEC	blood vessel
26	chr1:186281200-186338200	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr1:186281200-186341400	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr1:186281200-186341800	Strong transcription	Adipose Nuclei	Adipose
29	chr1:186281200-186342200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:186281200-186342200	Strong transcription	NH-A	brain
31	chr1:186281400-186341600	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr1:186281400-186342000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:186281400-186342000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr1:186281400-186342000	Strong transcription	Duodenum Mucosa	Duodenum
35	chr1:186281400-186342200	Strong transcription	Hela-S3	cervix
36	chr1:186281400-186342400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:186281400-186342600	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr1:186281800-186335600	Strong transcription	HMEC	breast
39	chr1:186281800-186342200	Strong transcription	K562	blood
40	chr1:186282400-186319600	Weak transcription	Stomach Mucosa	stomach
41	chr1:186283400-186341000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr1:186283800-186327800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:186285200-186342200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:186287000-186343400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr1:186288000-186319000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr1:186290000-186342000	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr1:186293200-186340000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr1:186293800-186340400	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr1:186294400-186341000	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr1:186294800-186338800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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