Variant report

Variant	rs12082399
Chromosome Location	chr1:186374412-186374413
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:186373972..186376157-chr1:186379499..186382713,3	MCF-7	breast:
2	chr1:186372550..186374489-chr1:186441138..186443259,2	MCF-7	breast:
3	chr1:186373731..186374559-chr1:186954735..186955602,2	MCF-7	breast:
4	chr1:186343109..186345591-chr1:186373069..186376266,4	K562	blood:
5	chr1:186374114..186376141-chr1:186408577..186410656,2	MCF-7	breast:
6	chr1:186361659..186366010-chr1:186371455..186375319,4	K562	blood:

Variant related genes	Relation type
ENSG00000047410	Chromatin interaction
ENSG00000268662	Chromatin interaction
ENSG00000157181	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1003127	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[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911847	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10911849	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10911854	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10911858	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[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582844	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12064371	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12068740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12069419	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12078527	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12084264	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12085497	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12093440	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1547084	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17580052	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2037959	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2273779	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2383479	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2383480	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3737940	0.87[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3753564	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3753567	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61810289	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61810292	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61831150	0.88[EUR][1000 genomes]
rs61831151	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7519719	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7539128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];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	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

No data

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	chr1:186348600-186390200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:186355600-186379200	Strong transcription	K562	blood
12	chr1:186355600-186381800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:186360000-186379200	Weak transcription	NHLF	lung
14	chr1:186361200-186375000	Weak transcription	HepG2	liver
15	chr1:186361400-186377000	Weak transcription	Fetal Heart	heart
16	chr1:186361600-186388400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:186362400-186405600	Weak transcription	Brain Angular Gyrus	brain
18	chr1:186362800-186375400	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:186362800-186378200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:186362800-186378400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr1:186362800-186405600	Weak transcription	Right Ventricle	heart
22	chr1:186363000-186378200	Weak transcription	Thymus	Thymus
23	chr1:186363600-186375200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:186364000-186376400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:186364600-186381600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:186365000-186375600	Strong transcription	Fetal Muscle Trunk	muscle
27	chr1:186365400-186390200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr1:186365600-186388000	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:186365600-186395200	Weak transcription	Psoas Muscle	Psoas
30	chr1:186365800-186388000	Weak transcription	Aorta	Aorta
31	chr1:186365800-186388000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr1:186365800-186388000	Weak transcription	Rectal Smooth Muscle	rectum
33	chr1:186366200-186393800	Weak transcription	Lung	lung
34	chr1:186366400-186388000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr1:186367000-186381000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:186367600-186375200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr1:186367600-186378400	Weak transcription	Ovary	ovary
38	chr1:186367600-186390000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr1:186367800-186387800	Weak transcription	Fetal Brain Male	brain
40	chr1:186368200-186388000	Weak transcription	Brain Substantia Nigra	brain
41	chr1:186368600-186375400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:186368600-186375800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr1:186368600-186376000	Weak transcription	Fetal Brain Female	brain
44	chr1:186368600-186378000	Weak transcription	Left Ventricle	heart
45	chr1:186368600-186398200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:186368800-186375000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr1:186368800-186387800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr1:186370200-186374600	Weak transcription	Brain Germinal Matrix	brain
49	chr1:186370200-186375000	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr1:186370200-186375800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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