Variant report

Variant	rs2249838
Chromosome Location	chr12:116957960-116957961
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:116942964..116945546-chr12:116956553..116958093,2	MCF-7	breast:
2	chr12:116950404..116952601-chr12:116956364..116958476,2	MCF-7	breast:
3	chr12:116957046..116958722-chr12:116975166..116976797,2	MCF-7	breast:
4	chr12:116957719..116961102-chr12:116962028..116965951,3	MCF-7	breast:
5	chr12:116957647..116960396-chr12:116971496..116974230,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196668	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1241229	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2733638	0.90[EUR][1000 genomes]
rs2733639	0.88[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	nsv899540	chr12:116920503-116999861	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:116946600-116970400	Weak transcription	Esophagus	oesophagus
2	chr12:116946800-116959200	Weak transcription	Right Atrium	heart
3	chr12:116952600-116958600	Weak transcription	Thymus	Thymus
4	chr12:116954000-116958600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:116954000-116959000	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr12:116954400-116968400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr12:116956600-116958400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:116956600-116958600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:116956600-116958600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr12:116956600-116958800	Weak transcription	A549	lung
11	chr12:116956800-116958000	Weak transcription	Fetal Thymus	thymus
12	chr12:116956800-116958600	Enhancers	NHEK	skin
13	chr12:116956800-116962200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:116957000-116958200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:116957000-116958600	Enhancers	HMEC	breast
16	chr12:116957200-116958600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr12:116957600-116958000	Enhancers	Primary B cells from peripheral blood	blood
18	chr12:116957600-116958400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:116957600-116958600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:116957600-116962400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:116957800-116958600	Weak transcription	Fetal Brain Female	brain
22	chr12:116957800-116959600	Enhancers	Fetal Brain Male	brain

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