Variant report

Variant	rs1689508
Chromosome Location	chr12:56310088-56310089
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56308199..56310170-chr12:56365833..56368306,2	MCF-7	breast:
2	chr12:56306449..56310619-chr12:56320899..56323064,5	MCF-7	breast:
3	chr12:56308254..56310551-chr12:56312979..56314818,2	MCF-7	breast:
4	chr12:56307549..56310271-chr12:56316708..56318919,2	MCF-7	breast:
5	chr12:56308633..56310681-chr12:56366386..56369249,2	MCF-7	breast:
6	chr12:56224193..56225056-chr12:56309266..56310167,2	MCF-7	breast:
7	chr12:56307383..56310841-chr12:56318368..56320626,3	K562	blood:
8	chr12:56210633..56213621-chr12:56308977..56310885,2	MCF-7	breast:
9	chr12:56299851..56302754-chr12:56309766..56311524,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000182796	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000205323	Chromatin interaction
ENSG00000111540	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1066130	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1068188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1068189	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1088050	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1091527	1.00[EUR][1000 genomes]
rs11829187	1.00[ASN][1000 genomes]
rs11831133	1.00[ASN][1000 genomes]
rs11833164	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11834873	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11835018	1.00[EUR][1000 genomes]
rs11835310	1.00[EUR][1000 genomes]
rs11838363	1.00[ASN][1000 genomes]
rs1626158	1.00[EUR][1000 genomes]
rs1681071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1681079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1681080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1681088	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1689509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1689517	1.00[EUR][1000 genomes]
rs1689518	1.00[EUR][1000 genomes]
rs1701701	1.00[EUR][1000 genomes]
rs1701702	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1702872	1.00[EUR][1000 genomes]
rs2035948	1.00[EUR][1000 genomes]
rs2046293	1.00[ASN][1000 genomes]
rs2625137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2625146	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2640566	1.00[EUR][1000 genomes]
rs2640568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2658478	1.00[EUR][1000 genomes]
rs2661728	1.00[EUR][1000 genomes]
rs2661729	1.00[EUR][1000 genomes]
rs2934152	1.00[EUR][1000 genomes]
rs34323718	1.00[EUR][1000 genomes]
rs4417324	1.00[EUR][1000 genomes]
rs56696262	1.00[EUR][1000 genomes]
rs57237559	1.00[EUR][1000 genomes]
rs57785224	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57990974	1.00[EUR][1000 genomes]
rs59794023	1.00[EUR][1000 genomes]
rs61733171	1.00[EUR][1000 genomes]
rs705697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705710	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705712	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705713	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705714	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705716	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705717	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7298109	1.00[EUR][1000 genomes]
rs7300292	1.00[EUR][1000 genomes]
rs7304690	1.00[EUR][1000 genomes]
rs7309327	1.00[EUR][1000 genomes]
rs7310292	1.00[EUR][1000 genomes]
rs73336393	1.00[ASN][1000 genomes]
rs73336399	1.00[ASN][1000 genomes]
rs73336402	1.00[ASN][1000 genomes]
rs73338377	1.00[EUR][1000 genomes]
rs73338385	1.00[EUR][1000 genomes]
rs772459	1.00[EUR][1000 genomes]
rs772463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs772464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs772467	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs772470	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs772474	1.00[EUR][1000 genomes]
rs772697	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs772698	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs772699	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs772701	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs772705	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954155	1.00[EUR][1000 genomes]
rs7957187	1.00[EUR][1000 genomes]
rs7958958	1.00[EUR][1000 genomes]
rs7975037	1.00[EUR][1000 genomes]
rs7980782	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 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	chr12:56279800-56320000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:56285200-56320000	Weak transcription	Pancreas	Pancrea
3	chr12:56291400-56319000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:56292800-56316000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:56293600-56319200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:56293800-56319600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr12:56294200-56319400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:56294400-56313800	Weak transcription	Ovary	ovary
9	chr12:56294400-56319600	Weak transcription	Colon Smooth Muscle	Colon
10	chr12:56296000-56319600	Weak transcription	Right Ventricle	heart
11	chr12:56296200-56319400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr12:56296800-56319600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr12:56297000-56315800	Weak transcription	Aorta	Aorta
14	chr12:56297200-56315600	Weak transcription	Fetal Brain Female	brain
15	chr12:56297200-56315600	Weak transcription	Lung	lung
16	chr12:56297200-56315800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr12:56297200-56319200	Weak transcription	Colonic Mucosa	Colon
18	chr12:56297200-56319600	Weak transcription	Brain Germinal Matrix	brain
19	chr12:56297200-56319600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr12:56297200-56320000	Weak transcription	Gastric	stomach
21	chr12:56297200-56320000	Weak transcription	Spleen	Spleen
22	chr12:56297400-56313000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:56297400-56315800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr12:56297400-56316000	Weak transcription	Thymus	Thymus
25	chr12:56297600-56319600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr12:56298000-56310400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:56300400-56319400	Weak transcription	HSMMtube	muscle
28	chr12:56303400-56319600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr12:56303600-56319600	Weak transcription	Brain Angular Gyrus	brain
30	chr12:56303800-56310200	Weak transcription	K562	blood
31	chr12:56303800-56315800	Weak transcription	Brain Substantia Nigra	brain
32	chr12:56303800-56319400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:56303800-56319400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr12:56303800-56319600	Weak transcription	Brain Anterior Caudate	brain
35	chr12:56304000-56319600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:56305600-56311600	Strong transcription	Fetal Thymus	thymus
37	chr12:56306000-56310400	Weak transcription	Fetal Brain Male	brain
38	chr12:56306200-56310400	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr12:56306200-56310400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:56306400-56310600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:56306600-56311000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:56306800-56310200	Strong transcription	Primary B cells from cord blood	blood
43	chr12:56306800-56311600	Strong transcription	Fetal Muscle Leg	muscle
44	chr12:56307200-56313800	Weak transcription	Left Ventricle	heart
45	chr12:56307400-56315800	Weak transcription	Adipose Nuclei	Adipose
46	chr12:56307400-56319400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr12:56307600-56315600	Weak transcription	Osteobl	bone
48	chr12:56307600-56319600	Weak transcription	Fetal Kidney	kidney
49	chr12:56307800-56310200	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr12:56307800-56310400	Enhancers	HMEC	breast

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