Variant report

Variant	rs2625146
Chromosome Location	chr12:56312988-56312989
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56305804..56307679-chr12:56311873..56314726,2	K562	blood:
2	chr12:56308254..56310551-chr12:56312979..56314818,2	MCF-7	breast:
3	chr12:56217992..56226798-chr12:56311494..56331042,68	MCF-7	breast:
4	chr12:56223538..56225484-chr12:56312926..56314904,2	MCF-7	breast:
5	chr12:56311836..56314158-chr12:56359202..56361497,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185664	Chromatin interaction
ENSG00000257390	Chromatin interaction
ENSG00000123374	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000258554	Chromatin interaction
ENSG00000135392	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	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1068188	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1068189	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1088050	1.00[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	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1681079	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1681080	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1681088	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1689508	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1689509	0.97[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	1.00[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	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	0.97[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	1.00[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	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705713	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705716	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705717	1.00[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	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs772464	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs772467	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs772470	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs772474	1.00[EUR][1000 genomes]
rs772697	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs772698	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs772699	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs772701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs772705	1.00[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:122 , 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	chr12:56300400-56319400	Weak transcription	HSMMtube	muscle
27	chr12:56303400-56319600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr12:56303600-56319600	Weak transcription	Brain Angular Gyrus	brain
29	chr12:56303800-56315800	Weak transcription	Brain Substantia Nigra	brain
30	chr12:56303800-56319400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:56303800-56319400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr12:56303800-56319600	Weak transcription	Brain Anterior Caudate	brain
33	chr12:56304000-56319600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:56307200-56313800	Weak transcription	Left Ventricle	heart
35	chr12:56307400-56315800	Weak transcription	Adipose Nuclei	Adipose
36	chr12:56307400-56319400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr12:56307600-56315600	Weak transcription	Osteobl	bone
38	chr12:56307600-56319600	Weak transcription	Fetal Kidney	kidney
39	chr12:56307800-56315400	Weak transcription	Placenta	Placenta
40	chr12:56307800-56316000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:56308000-56315800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr12:56308000-56319600	Weak transcription	Brain Hippocampus Middle	brain
43	chr12:56308200-56313800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr12:56308200-56314600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr12:56308200-56315600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr12:56308200-56315600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:56308200-56315600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr12:56308200-56319400	Weak transcription	HSMM	muscle
49	chr12:56308400-56315400	Weak transcription	Fetal Intestine Large	intestine
50	chr12:56308400-56315800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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