Variant report

Variant	rs10877859
Chromosome Location	chr12:62873873-62873874
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:62873316..62875868-chr12:62879618..62881508,2	MCF-7	breast:
2	chr12:62872291..62875006-chr12:62876565..62879431,3	K562	blood:
3	chr12:62859530..62861821-chr12:62870418..62875457,4	MCF-7	breast:
4	chr12:62872795..62875002-chr12:62880662..62883427,2	K562	blood:
5	chr12:62873508..62875169-chr12:62896381..62898756,2	K562	blood:

Variant related genes	Relation type
ENSG00000061987	Chromatin interaction
ENSG00000257568	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10877855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877856	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877857	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877864	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877870	0.94[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174487	0.86[CEU][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11174494	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174495	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174496	0.91[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174498	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174504	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174514	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174517	0.93[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174518	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174527	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174537	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11174557	0.87[CEU][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11174562	0.82[AFR][1000 genomes]
rs11174568	0.91[AFR][1000 genomes]
rs11174571	0.81[CEU][hapmap];0.91[AFR][1000 genomes]
rs11174575	0.91[AFR][1000 genomes]
rs11520127	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11613132	0.93[CEU][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11614022	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11614822	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12367878	0.91[AFR][1000 genomes]
rs12369751	0.91[AFR][1000 genomes]
rs12369961	0.88[CEU][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12369985	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12370404	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17731893	0.82[AFR][1000 genomes]
rs17732089	0.80[CEU][hapmap];0.82[AFR][1000 genomes]
rs17732182	0.91[AFR][1000 genomes]
rs55833440	0.82[AFR][1000 genomes]
rs7296573	0.91[AFR][1000 genomes]
rs7297093	0.91[AFR][1000 genomes]
rs7301016	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302094	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7302456	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7303825	0.94[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73124315	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73126004	0.82[AFR][1000 genomes]
rs73126024	0.91[AFR][1000 genomes]
rs73141014	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73141045	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7962519	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975109	0.93[CEU][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530690	chr12:62678463-62999462	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv899158	chr12:62783967-62937259	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv899159	chr12:62783967-62945245	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv821671	chr12:62794304-63007964	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62861800-62879800	Weak transcription	HSMMtube	muscle
2	chr12:62861800-62902200	Weak transcription	Fetal Kidney	kidney
3	chr12:62862800-62895400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:62863200-62875600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:62863200-62875600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr12:62863200-62875600	Weak transcription	Gastric	stomach
7	chr12:62863200-62876000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:62863200-62879400	Weak transcription	Thymus	Thymus
9	chr12:62863200-62881400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:62863200-62895200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr12:62863200-62896800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr12:62863200-62901800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr12:62863200-62937400	Weak transcription	Pancreas	Pancrea
14	chr12:62863400-62874000	Weak transcription	Hela-S3	cervix
15	chr12:62863400-62875600	Weak transcription	Brain Angular Gyrus	brain
16	chr12:62863400-62877600	Weak transcription	A549	lung
17	chr12:62863400-62878200	Weak transcription	Fetal Lung	lung
18	chr12:62863400-62895400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:62863400-62902000	Weak transcription	HUVEC	blood vessel
20	chr12:62863400-62911000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr12:62863600-62874200	Weak transcription	Brain Substantia Nigra	brain
22	chr12:62863600-62875400	Weak transcription	Brain Anterior Caudate	brain
23	chr12:62863600-62875600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr12:62863600-62877400	Weak transcription	NHEK	skin
25	chr12:62863600-62892600	Weak transcription	NH-A	brain
26	chr12:62863600-62926400	Weak transcription	Colon Smooth Muscle	Colon
27	chr12:62864000-62874200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr12:62864000-62874200	Weak transcription	Dnd41	blood
29	chr12:62864000-62874400	Weak transcription	Colonic Mucosa	Colon
30	chr12:62864000-62874400	Weak transcription	HMEC	breast
31	chr12:62864000-62875400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr12:62864000-62878800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr12:62864000-62894400	Weak transcription	Spleen	Spleen
34	chr12:62864000-62899200	Weak transcription	Brain Germinal Matrix	brain
35	chr12:62864000-62901600	Weak transcription	Lung	lung
36	chr12:62864000-62901600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr12:62864000-62906200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr12:62864600-62875400	Weak transcription	Brain Hippocampus Middle	brain
39	chr12:62865800-62876000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr12:62866000-62892000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:62866000-62895400	Weak transcription	Left Ventricle	heart
42	chr12:62866200-62887400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr12:62866200-62897000	Weak transcription	K562	blood
44	chr12:62866200-62899200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr12:62866200-62906200	Weak transcription	Aorta	Aorta
46	chr12:62866600-62875800	Weak transcription	Right Ventricle	heart
47	chr12:62866600-62877600	Weak transcription	NHDF-Ad	bronchial
48	chr12:62866600-62896000	Weak transcription	Fetal Brain Female	brain
49	chr12:62866600-62906200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr12:62866600-62912400	Weak transcription	NHLF	lung

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