Variant report

Variant	rs13377661
Chromosome Location	chr12:11885175-11885176
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:11800555..11803828-chr12:11880489..11886142,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139083	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10491988	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10491989	1.00[AMR][1000 genomes]
rs11054431	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12303444	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12310333	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2051525	0.81[LWK][hapmap]
rs2710267	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2724598	1.00[EUR][1000 genomes]
rs2724602	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2724637	1.00[EUR][1000 genomes]
rs2856340	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs55682120	1.00[AMR][1000 genomes]
rs57222202	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59302227	1.00[EUR][1000 genomes]
rs7133092	1.00[EUR][1000 genomes]
rs7302827	1.00[EUR][1000 genomes]
rs7307437	1.00[EUR][1000 genomes]
rs73288792	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74060832	1.00[AMR][1000 genomes]
rs74060834	1.00[AMR][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	nsv870039	chr12:11800363-11996598	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11873200-11902400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:11873200-11909400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:11873400-11894200	Weak transcription	NHLF	lung
4	chr12:11874200-11885400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr12:11875000-11888600	Enhancers	Primary B cells from peripheral blood	blood
6	chr12:11876800-11885800	Enhancers	Pancreas	Pancrea
7	chr12:11877400-11886600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:11878000-11888600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:11878000-11889600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr12:11878800-11886200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:11879200-11886000	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr12:11879800-11885800	Enhancers	HMEC	breast
13	chr12:11880400-11885600	Enhancers	Fetal Intestine Large	intestine
14	chr12:11880400-11885800	Enhancers	Thymus	Thymus
15	chr12:11880400-11896200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:11880600-11885200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:11880600-11896400	Weak transcription	Fetal Stomach	stomach
18	chr12:11880800-11890800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:11881000-11885400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:11881000-11885600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:11882200-11888400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:11882400-11899200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:11882400-11902600	Weak transcription	Fetal Muscle Leg	muscle
24	chr12:11882400-11903200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr12:11882800-11885400	Enhancers	Placenta Amnion	Placenta Amnion
26	chr12:11882800-11885800	Enhancers	Small Intestine	intestine
27	chr12:11883000-11885200	Enhancers	Primary hematopoietic stem cells	blood
28	chr12:11883200-11885200	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr12:11883200-11885600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr12:11883200-11885800	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr12:11883200-11894400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr12:11883400-11885200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:11883400-11885800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:11883600-11885400	Enhancers	NH-A	brain
35	chr12:11883600-11885600	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr12:11883600-11889600	Weak transcription	Fetal Kidney	kidney
37	chr12:11883600-11891400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr12:11883600-11891400	Weak transcription	Right Ventricle	heart
39	chr12:11883600-11894000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr12:11883600-11896200	Weak transcription	Colon Smooth Muscle	Colon
41	chr12:11883800-11885200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr12:11883800-11885200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:11883800-11885200	Enhancers	Osteobl	bone
44	chr12:11883800-11885400	Enhancers	Muscle Satellite Cultured Cells	--
45	chr12:11883800-11885600	Enhancers	Stomach Mucosa	stomach
46	chr12:11883800-11906000	Weak transcription	Liver	Liver
47	chr12:11884000-11885400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr12:11884000-11894000	Weak transcription	Right Atrium	heart
49	chr12:11884000-11894200	Weak transcription	Psoas Muscle	Psoas
50	chr12:11884200-11885800	Enhancers	Duodenum Mucosa	Duodenum

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