Variant report

Variant	rs12306670
Chromosome Location	chr12:56557828-56557829
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56437997..56440077-chr12:56556609..56558921,2	K562	blood:
2	chr12:56519569..56524417-chr12:56555136..56559386,7	MCF-7	breast:
3	chr12:56507747..56515530-chr12:56549896..56559767,36	MCF-7	breast:
4	chr12:56557531..56560947-chr12:56576464..56579255,4	MCF-7	breast:
5	chr12:56555575..56559799-chr12:56572215..56575124,4	MCF-7	breast:
6	chr12:56508092..56528020-chr12:56536122..56568603,201	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229117	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000258317	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000139613	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11171753	1.00[TSI][hapmap]
rs11171760	1.00[EUR][1000 genomes]
rs11171772	1.00[AMR][1000 genomes]
rs11171777	1.00[TSI][hapmap]
rs11834728	1.00[TSI][hapmap]
rs11837267	1.00[EUR][1000 genomes]
rs12298822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12308473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12316272	0.89[AFR][1000 genomes]
rs12320265	0.82[ASW][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1405859	1.00[AMR][1000 genomes]
rs17852368	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2450101	1.00[EUR][1000 genomes]
rs2463365	1.00[TSI][hapmap]
rs2629453	1.00[EUR][1000 genomes]
rs2695783	1.00[TSI][hapmap]
rs2695784	1.00[TSI][hapmap]
rs28546848	1.00[EUR][1000 genomes]
rs2930788	1.00[TSI][hapmap]
rs55887836	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56163805	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59499104	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60011575	0.85[AFR][1000 genomes]
rs703823	1.00[TSI][hapmap]
rs7136420	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs73340385	1.00[EUR][1000 genomes]
rs73340390	1.00[EUR][1000 genomes]
rs7397951	1.00[EUR][1000 genomes]
rs74092003	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7489249	1.00[TSI][hapmap]
rs772925	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs772926	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs773654	1.00[EUR][1000 genomes]
rs773658	1.00[TSI][hapmap]
rs773659	1.00[TSI][hapmap]
rs773663	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7962107	1.00[ASW][hapmap];0.85[LWK][hapmap]
rs7967464	1.00[EUR][1000 genomes]
rs7975486	1.00[TSI][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56554000-56582000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:56554200-56581400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:56554600-56558200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:56554600-56568600	Strong transcription	Ovary	ovary
5	chr12:56555000-56558400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:56555000-56569600	Strong transcription	Brain Substantia Nigra	brain
7	chr12:56555000-56575600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr12:56555000-56579800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:56555000-56580800	Strong transcription	H9 Cell Line	embryonic stem cell
10	chr12:56555000-56580800	Strong transcription	Brain Anterior Caudate	brain
11	chr12:56555000-56581000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:56555200-56559600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:56555200-56559600	Strong transcription	Small Intestine	intestine
14	chr12:56555200-56560600	Strong transcription	Lung	lung
15	chr12:56555200-56562000	Strong transcription	Primary B cells from cord blood	blood
16	chr12:56555200-56563200	Weak transcription	Right Atrium	heart
17	chr12:56555200-56565200	Weak transcription	Fetal Brain Male	brain
18	chr12:56555200-56573600	Strong transcription	Fetal Lung	lung
19	chr12:56555200-56578800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr12:56555200-56580600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:56555200-56580800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr12:56555400-56558400	Strong transcription	Fetal Kidney	kidney
23	chr12:56555400-56559000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr12:56555400-56559800	Strong transcription	Aorta	Aorta
25	chr12:56555400-56559800	Strong transcription	Hela-S3	cervix
26	chr12:56555400-56560200	Strong transcription	Primary T cells from cord blood	blood
27	chr12:56555400-56568600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr12:56555400-56568600	Strong transcription	Esophagus	oesophagus
29	chr12:56555400-56568600	Strong transcription	Gastric	stomach
30	chr12:56555400-56579000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
31	chr12:56555400-56580000	Strong transcription	Placenta	Placenta
32	chr12:56555400-56580600	Strong transcription	Thymus	Thymus
33	chr12:56555400-56580800	Strong transcription	Primary B cells from peripheral blood	blood
34	chr12:56555400-56580800	Strong transcription	Brain Inferior Temporal Lobe	brain
35	chr12:56555400-56580800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr12:56555600-56559800	Strong transcription	K562	blood
37	chr12:56555600-56561200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr12:56555600-56566600	Strong transcription	Spleen	Spleen
39	chr12:56555600-56569000	Strong transcription	Left Ventricle	heart
40	chr12:56555600-56573600	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr12:56555600-56575400	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr12:56555600-56576000	Strong transcription	Brain Cingulate Gyrus	brain
43	chr12:56555600-56580600	Strong transcription	Fetal Brain Female	brain
44	chr12:56555600-56580800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr12:56555600-56580800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr12:56555600-56580800	Strong transcription	Liver	Liver
47	chr12:56555600-56580800	Strong transcription	Osteobl	bone
48	chr12:56555800-56559000	Strong transcription	Fetal Muscle Trunk	muscle
49	chr12:56555800-56559200	Strong transcription	Brain Hippocampus Middle	brain
50	chr12:56555800-56560400	Strong transcription	Right Ventricle	heart

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