Variant report

Variant	rs11806304
Chromosome Location	chr1:186372865-186372866
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:186372550..186374489-chr1:186441138..186443259,2	MCF-7	breast:
2	chr1:186303450..186305307-chr1:186372043..186373859,2	K562	blood:
3	chr1:186370487..186373941-chr1:186374883..186377860,4	K562	blood:
4	chr1:186351329..186353389-chr1:186372131..186374033,2	K562	blood:
5	chr1:186361659..186366010-chr1:186371455..186375319,4	K562	blood:

Variant related genes	Relation type
ENSG00000268662	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11799811	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11799843	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11801527	0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.82[ASN][1000 genomes]
rs11803944	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.86[ASN][1000 genomes]
rs11805289	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11805302	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11806068	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11809402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811320	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11812050	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs12723621	0.91[TSI][hapmap]
rs12726960	0.82[CEU][hapmap]
rs12728791	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12733799	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[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12739797	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]
rs12740221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12742751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12747113	0.86[ASN][1000 genomes]
rs12749203	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12750686	0.83[AFR][1000 genomes]
rs12752376	0.86[ASN][1000 genomes]
rs16825361	0.86[ASN][1000 genomes]
rs16825403	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs1919194	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2273774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2273775	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2293569	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2293570	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34467087	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34552348	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs34924250	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35131069	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35146131	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35326401	0.84[ASN][1000 genomes]
rs35942197	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3766698	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766701	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3817586	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];0.80[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4140432	0.92[TSI][hapmap]
rs57716405	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58626385	0.83[ASN][1000 genomes]
rs6674145	0.82[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap]
rs6682896	0.82[CHD][hapmap]
rs71634159	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71634161	0.86[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	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	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
4	nsv1012164	chr1:186323867-186565995	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	esv2762201	chr1:186323879-186566007	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv872589	chr1:186354146-186390303	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	esv1824284	chr1:186358588-186441585	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11806304	TSEN15	cis	parietal	SCAN
rs11806304	NCF2	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186345400-186390600	Weak transcription	Small Intestine	intestine
2	chr1:186345400-186398200	Weak transcription	Spleen	Spleen
3	chr1:186345800-186377400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:186346200-186380400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:186346200-186388400	Weak transcription	Colonic Mucosa	Colon
6	chr1:186346400-186376000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:186346400-186388000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:186346400-186390000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:186348000-186382000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:186348600-186373400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:186348600-186390200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:186349200-186373200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr1:186349600-186373200	Strong transcription	Duodenum Mucosa	Duodenum
14	chr1:186355600-186379200	Strong transcription	K562	blood
15	chr1:186355600-186381800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:186357400-186373400	Strong transcription	Liver	Liver
17	chr1:186357600-186373200	Strong transcription	Placenta	Placenta
18	chr1:186360000-186374400	Weak transcription	Fetal Lung	lung
19	chr1:186360000-186379200	Weak transcription	NHLF	lung
20	chr1:186361200-186375000	Weak transcription	HepG2	liver
21	chr1:186361400-186377000	Weak transcription	Fetal Heart	heart
22	chr1:186361600-186388400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:186362400-186405600	Weak transcription	Brain Angular Gyrus	brain
24	chr1:186362800-186375400	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:186362800-186378200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr1:186362800-186378400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr1:186362800-186405600	Weak transcription	Right Ventricle	heart
28	chr1:186363000-186378200	Weak transcription	Thymus	Thymus
29	chr1:186363600-186375200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:186364000-186376400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:186364600-186381600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:186365000-186375600	Strong transcription	Fetal Muscle Trunk	muscle
33	chr1:186365400-186390200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr1:186365600-186374400	Weak transcription	NHEK	skin
35	chr1:186365600-186388000	Weak transcription	Brain Hippocampus Middle	brain
36	chr1:186365600-186395200	Weak transcription	Psoas Muscle	Psoas
37	chr1:186365800-186388000	Weak transcription	Aorta	Aorta
38	chr1:186365800-186388000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr1:186365800-186388000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr1:186366200-186393800	Weak transcription	Lung	lung
41	chr1:186366400-186374400	Weak transcription	Fetal Kidney	kidney
42	chr1:186366400-186388000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr1:186367000-186381000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr1:186367200-186374400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:186367200-186374400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr1:186367600-186375200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr1:186367600-186378400	Weak transcription	Ovary	ovary
48	chr1:186367600-186390000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr1:186367800-186387800	Weak transcription	Fetal Brain Male	brain
50	chr1:186368200-186388000	Weak transcription	Brain Substantia Nigra	brain

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