Variant report

Variant	rs12319401
Chromosome Location	chr12:10780338-10780339
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:10765473..10767924-chr12:10779582..10781462,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111196	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11053888	1.00[ASW][hapmap];0.89[LWK][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11053890	0.80[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11053891	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11836109	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11836264	0.90[AMR][1000 genomes]
rs12297620	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs12299672	0.80[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12302213	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12304304	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs12304656	1.00[ASW][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12311784	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12315090	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12315191	0.81[AFR][1000 genomes]
rs12321785	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12322680	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs2198964	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55785135	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs56801111	0.81[AMR][1000 genomes]
rs57025730	0.81[AMR][1000 genomes]
rs57035205	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs58067632	0.81[AMR][1000 genomes]
rs58677311	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs59613394	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs60400937	0.81[AMR][1000 genomes]
rs60461379	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs61473048	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7303851	1.00[ASW][hapmap]
rs73252005	0.81[AMR][1000 genomes]
rs73254038	0.81[AMR][1000 genomes]
rs74060455	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs74060471	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs74060473	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7968001	0.88[AFR][1000 genomes];0.90[AMR][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	nsv832329	chr12:10677094-10845946	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv607	chr12:10776867-10821535	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10766600-10787000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:10766600-10789400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:10766600-10794400	Weak transcription	Gastric	stomach
4	chr12:10766800-10789400	Weak transcription	Esophagus	oesophagus
5	chr12:10767200-10780600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr12:10767200-10781200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr12:10771400-10782200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr12:10772000-10787200	Weak transcription	NHEK	skin
9	chr12:10772400-10780600	Weak transcription	HMEC	breast
10	chr12:10773000-10786600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:10773000-10787000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:10773400-10787000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:10774600-10784000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr12:10774600-10784400	Weak transcription	HSMMtube	muscle
15	chr12:10775200-10780600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr12:10776200-10784200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:10776200-10785200	Weak transcription	HSMM	muscle
18	chr12:10777200-10781000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:10777600-10784000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr12:10777600-10786600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:10777600-10787400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:10777800-10780600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:10777800-10786400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:10778600-10782400	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr12:10779800-10790000	Strong transcription	HUVEC	blood vessel
26	chr12:10780200-10781200	Strong transcription	Sigmoid Colon	Sigmoid Colon

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