Variant report

Variant	rs888197
Chromosome Location	chr12:12628219-12628220
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: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10845553	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10845554	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10845557	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10845562	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10845565	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10845569	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs11054923	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11054925	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11054926	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11054935	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[ASN][1000 genomes]
rs11609905	0.81[ASN][1000 genomes]
rs11612508	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs12369319	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12424448	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12819116	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17312926	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17379216	1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2287206	0.83[CEU][hapmap]
rs2417189	0.81[EUR][1000 genomes]
rs2417191	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs736107	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs744170	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs747726	0.83[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes]
rs962927	0.89[GIH][hapmap];0.80[MEX][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs888197	CLEC2B	cis	cerebellum	SCAN
rs888197	ETV6	cis	cerebellum	SCAN
rs888197	AICDA	cis	cerebellum	SCAN
rs888197	LOH12CR1	cis	parietal	SCAN

Chromatin state (count:122 , 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	chr12:12609800-12628400	Weak transcription	NHLF	lung
8	chr12:12610800-12658000	Weak transcription	NHDF-Ad	bronchial
9	chr12:12611000-12628600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:12611200-12629000	Weak transcription	Hela-S3	cervix
11	chr12:12616400-12629800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:12617000-12628800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:12618400-12642200	Weak transcription	Stomach Mucosa	stomach
14	chr12:12618800-12629800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:12619000-12629200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:12619000-12634000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr12:12619400-12629200	Weak transcription	Right Ventricle	heart
18	chr12:12620000-12629000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:12621000-12628400	Weak transcription	Aorta	Aorta
20	chr12:12621000-12629000	Weak transcription	Osteobl	bone
21	chr12:12621000-12630000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr12:12621200-12629000	Weak transcription	Ovary	ovary
23	chr12:12621200-12629000	Weak transcription	HSMM	muscle
24	chr12:12621400-12628400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr12:12621400-12628600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr12:12621400-12629200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:12621400-12636000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr12:12621400-12645400	Weak transcription	Small Intestine	intestine
29	chr12:12621600-12628800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr12:12621600-12635800	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr12:12621600-12646000	Weak transcription	Psoas Muscle	Psoas
32	chr12:12621600-12646200	Weak transcription	Brain Germinal Matrix	brain
33	chr12:12621800-12634000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr12:12622600-12653800	Weak transcription	Fetal Heart	heart
35	chr12:12622800-12629800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:12623000-12628800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr12:12623600-12629200	Weak transcription	Fetal Brain Female	brain
38	chr12:12624000-12629000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:12624000-12638000	Weak transcription	HMEC	breast
40	chr12:12624400-12632800	Weak transcription	Primary B cells from cord blood	blood
41	chr12:12624600-12629400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr12:12624600-12630000	Weak transcription	Primary B cells from peripheral blood	blood
43	chr12:12625000-12628400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr12:12625200-12634000	Strong transcription	Fetal Intestine Small	intestine
45	chr12:12626000-12635800	Strong transcription	Fetal Intestine Large	intestine
46	chr12:12626200-12628400	Enhancers	Brain Hippocampus Middle	brain
47	chr12:12626200-12634600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr12:12626400-12628400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr12:12626400-12628800	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr12:12626400-12629400	Enhancers	Primary T helper naive cells from peripheral blood	blood

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