Variant report

Variant	rs6539236
Chromosome Location	chr12:106325317-106325318
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:106252103..106254778-chr12:106324324..106327304,2	MCF-7	breast:
2	chr12:106290453..106292441-chr12:106325256..106328012,2	MCF-7	breast:
3	chr12:106315789..106319466-chr12:106324083..106326577,3	MCF-7	breast:
4	chr12:106252576..106257330-chr12:106324880..106330173,10	MCF-7	breast:
5	chr12:106322923..106333063-chr12:106528610..106534226,20	MCF-7	breast:

Variant related genes	Relation type
ENSG00000074590	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10507205	1.00[EUR][1000 genomes]
rs11112802	1.00[EUR][1000 genomes]
rs11112811	1.00[EUR][1000 genomes]
rs12301159	1.00[EUR][1000 genomes]
rs12311347	1.00[EUR][1000 genomes]
rs12314342	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs13378063	1.00[EUR][1000 genomes]
rs1421450	1.00[EUR][1000 genomes]
rs17037848	1.00[EUR][1000 genomes]
rs17037959	1.00[EUR][1000 genomes]
rs17037993	1.00[EUR][1000 genomes]
rs17038001	1.00[EUR][1000 genomes]
rs17038024	1.00[EUR][1000 genomes]
rs34404995	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41513347	1.00[EUR][1000 genomes]
rs7135356	0.87[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7298805	1.00[EUR][1000 genomes]
rs7299337	1.00[EUR][1000 genomes]
rs7312705	1.00[EUR][1000 genomes]
rs73391203	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73391208	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73391222	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs744346	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs744347	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7968919	0.85[AMR][1000 genomes];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	nsv832508	chr12:106198797-106409112	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2761768	chr12:106317265-106326204	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106317000-106327600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:106317200-106325800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr12:106321200-106327600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:106322000-106325400	Weak transcription	Esophagus	oesophagus
5	chr12:106322000-106325800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:106322200-106327600	Weak transcription	HSMM	muscle
7	chr12:106323000-106326200	Enhancers	Brain Germinal Matrix	brain
8	chr12:106323200-106325800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:106323200-106326800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr12:106323400-106325400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:106324000-106326400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:106324200-106326400	Enhancers	Fetal Muscle Leg	muscle
13	chr12:106324400-106325600	Enhancers	Fetal Heart	heart
14	chr12:106324400-106326400	Enhancers	Fetal Lung	lung
15	chr12:106324400-106326400	Genic enhancers	HSMMtube	muscle
16	chr12:106324400-106327800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr12:106324400-106327800	Enhancers	NHEK	skin
18	chr12:106324600-106325400	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr12:106324600-106326000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr12:106324600-106326200	Enhancers	K562	blood
21	chr12:106324600-106327800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr12:106324600-106327800	Weak transcription	Brain Substantia Nigra	brain
23	chr12:106324600-106332000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr12:106324800-106325400	Enhancers	Hela-S3	cervix
25	chr12:106324800-106326400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:106324800-106327600	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:106324800-106327800	Weak transcription	Brain Anterior Caudate	brain
28	chr12:106324800-106332200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr12:106324800-106332400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr12:106325000-106326000	Weak transcription	Lung	lung
31	chr12:106325000-106326400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:106325000-106327200	Weak transcription	HUVEC	blood vessel
33	chr12:106325000-106327600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:106325000-106327600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:106325000-106327600	Weak transcription	Psoas Muscle	Psoas
36	chr12:106325000-106327800	Weak transcription	Right Ventricle	heart
37	chr12:106325000-106329000	Weak transcription	Left Ventricle	heart
38	chr12:106325000-106329800	Weak transcription	Right Atrium	heart
39	chr12:106325200-106325400	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr12:106325200-106325600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr12:106325200-106325600	Weak transcription	HMEC	breast
42	chr12:106325200-106326200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr12:106325200-106326600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:106325200-106326600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr12:106325200-106327600	Weak transcription	A549	lung
46	chr12:106325200-106332400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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