Variant report

Variant	rs12492542
Chromosome Location	chr3:113368172-113368173
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	chr3:113366819..113369386-chr3:113414754..113416539,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176542	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10934239	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10934240	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11914863	1.00[ASN][1000 genomes]
rs11918910	1.00[ASN][1000 genomes]
rs11920913	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11921407	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs12486414	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12489192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12490048	0.93[AMR][1000 genomes]
rs12490651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12491540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12492290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12492783	0.93[AMR][1000 genomes]
rs12493602	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12493935	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12494777	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12495298	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12495713	1.00[AMR][1000 genomes]
rs12496604	1.00[AMR][1000 genomes]
rs12496617	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12497754	1.00[AMR][1000 genomes]
rs16861230	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16861233	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16861235	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16861331	1.00[AMR][1000 genomes]
rs2292512	1.00[MEX][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs2566972	0.85[MEX][hapmap];0.87[AMR][1000 genomes]
rs2603791	0.87[AMR][1000 genomes]
rs3773686	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs58929900	0.85[ASN][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	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113342600-113375800	Weak transcription	Pancreas	Pancrea
2	chr3:113365800-113368400	Weak transcription	Psoas Muscle	Psoas
3	chr3:113365800-113375200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr3:113366000-113373800	Weak transcription	Primary B cells from cord blood	blood
5	chr3:113366000-113373800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr3:113366000-113376200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr3:113366000-113377000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:113366000-113377000	Weak transcription	Liver	Liver
9	chr3:113366200-113368400	Weak transcription	Primary T cells from cord blood	blood
10	chr3:113366200-113373400	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr3:113366200-113373800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr3:113366200-113374400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:113366200-113375400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr3:113366400-113375800	Weak transcription	Spleen	Spleen
15	chr3:113366600-113369000	Enhancers	Rectal Smooth Muscle	rectum
16	chr3:113366600-113374800	Weak transcription	Fetal Intestine Large	intestine
17	chr3:113366800-113373800	Weak transcription	Aorta	Aorta
18	chr3:113366800-113378800	Weak transcription	Gastric	stomach
19	chr3:113367200-113373200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr3:113367200-113373600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:113367200-113374200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:113367200-113377600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr3:113367600-113368600	Enhancers	Colon Smooth Muscle	Colon
24	chr3:113367600-113368600	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr3:113368000-113368600	Enhancers	Fetal Lung	lung
26	chr3:113368000-113368600	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr3:113368000-113374400	Weak transcription	HSMMtube	muscle
28	chr3:113368000-113376200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:113368000-113376200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr3:113368000-113383400	Weak transcription	Colonic Mucosa	Colon

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