Variant report

Variant	rs10845552
Chromosome Location	chr12:12628565-12628566
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	chr12:12627656..12629793-chr12:12641466..12644358,2	MCF-7	breast:
2	chr12:12624389..12628986-chr12:12712843..12715997,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LOH12CR1-3	chr12:12626618-12628831	NONHSAT026972
2	lnc-DUSP16-1	chr12:12627157-12629731	NONHSAT026975

Variant related genes	Relation type
ENSG00000111266	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10743988	0.85[AMR][1000 genomes]
rs10845556	0.86[EUR][1000 genomes]
rs10845559	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes]
rs10845560	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes]
rs10845563	0.80[MEX][hapmap]
rs10845567	0.83[CEU][hapmap];0.89[CHB][hapmap];0.82[AMR][1000 genomes]
rs10845572	0.91[CHB][hapmap]
rs11054937	0.85[AMR][1000 genomes]
rs11054940	0.91[CHB][hapmap]
rs11054941	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes]
rs11054942	0.86[CHB][hapmap];0.91[MEX][hapmap]
rs11613385	0.91[CHB][hapmap]
rs12422540	0.87[CEU][hapmap];0.85[CHB][hapmap];0.88[AMR][1000 genomes]
rs2111271	0.88[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2287206	0.80[MEX][hapmap]
rs2417190	0.86[CHB][hapmap]
rs4255620	0.82[AMR][1000 genomes]
rs4763833	0.91[CHB][hapmap];0.91[MEX][hapmap]
rs7137455	0.86[CHB][hapmap]
rs7294378	0.84[AMR][1000 genomes]
rs7295305	0.86[CHB][hapmap];0.87[MEX][hapmap]
rs7310652	0.85[AMR][1000 genomes]
rs7972902	0.91[CHB][hapmap]
rs933575	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs962927	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs962928	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[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	esv2758295	chr12:12620654-12783124	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2759880	chr12:12620654-12783124	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10845552	ATF7IP	cis	cerebellum	SCAN
rs10845552	ETV6	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12596000-12629800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr12:12597400-12629000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr12:12603800-12639200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr12:12604000-12628600	Weak transcription	Fetal Lung	lung
5	chr12:12607800-12629400	Weak transcription	Fetal Kidney	kidney
6	chr12:12608400-12629600	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:12610800-12658000	Weak transcription	NHDF-Ad	bronchial
8	chr12:12611000-12628600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:12611200-12629000	Weak transcription	Hela-S3	cervix
10	chr12:12616400-12629800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:12617000-12628800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:12618400-12642200	Weak transcription	Stomach Mucosa	stomach
13	chr12:12618800-12629800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:12619000-12629200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:12619000-12634000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr12:12619400-12629200	Weak transcription	Right Ventricle	heart
17	chr12:12620000-12629000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:12621000-12629000	Weak transcription	Osteobl	bone
19	chr12:12621000-12630000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr12:12621200-12629000	Weak transcription	Ovary	ovary
21	chr12:12621200-12629000	Weak transcription	HSMM	muscle
22	chr12:12621400-12628600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr12:12621400-12629200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:12621400-12636000	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr12:12621400-12645400	Weak transcription	Small Intestine	intestine
26	chr12:12621600-12628800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:12621600-12635800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr12:12621600-12646000	Weak transcription	Psoas Muscle	Psoas
29	chr12:12621600-12646200	Weak transcription	Brain Germinal Matrix	brain
30	chr12:12621800-12634000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr12:12622600-12653800	Weak transcription	Fetal Heart	heart
32	chr12:12622800-12629800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:12623000-12628800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr12:12623600-12629200	Weak transcription	Fetal Brain Female	brain
35	chr12:12624000-12629000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr12:12624000-12638000	Weak transcription	HMEC	breast
37	chr12:12624400-12632800	Weak transcription	Primary B cells from cord blood	blood
38	chr12:12624600-12629400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr12:12624600-12630000	Weak transcription	Primary B cells from peripheral blood	blood
40	chr12:12625200-12634000	Strong transcription	Fetal Intestine Small	intestine
41	chr12:12626000-12635800	Strong transcription	Fetal Intestine Large	intestine
42	chr12:12626200-12634600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr12:12626400-12628800	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr12:12626400-12629400	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr12:12626400-12639000	Strong transcription	Placenta	Placenta
46	chr12:12626600-12631800	Genic enhancers	Brain Anterior Caudate	brain
47	chr12:12626600-12634400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr12:12626600-12636600	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr12:12626600-12636800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:12626600-12639200	Strong transcription	Liver	Liver

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