Variant report

Variant	rs12693551
Chromosome Location	chr2:190529231-190529232
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:190527802..190529526-chr2:190626576..190628968,2	MCF-7	breast:
2	chr2:190526059..190528358-chr2:190528591..190531443,4	MCF-7	breast:
3	chr2:190528985..190530799-chr2:190560086..190562548,2	K562	blood:

Variant related genes	Relation type
ENSG00000138381	Chromatin interaction
ENSG00000253559	Chromatin interaction
ENSG00000128694	Chromatin interaction
ENSG00000151687	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10195109	0.80[CEU][hapmap];0.87[JPT][hapmap]
rs10197331	0.84[EUR][1000 genomes]
rs10207346	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10210345	0.90[CEU][hapmap]
rs1055091	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs10931430	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10931431	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10931433	0.83[EUR][1000 genomes]
rs1132360	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11679767	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11685425	0.85[EUR][1000 genomes]
rs1225101	0.91[JPT][hapmap]
rs1233245	0.84[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap]
rs1233262	0.84[EUR][1000 genomes]
rs1233265	0.84[EUR][1000 genomes]
rs1233272	0.83[EUR][1000 genomes]
rs1233282	0.83[EUR][1000 genomes]
rs1233284	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs1233288	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs1233291	0.82[EUR][1000 genomes]
rs1233297	0.85[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs1233299	0.83[EUR][1000 genomes]
rs1233302	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs1234834	0.82[EUR][1000 genomes]
rs12471217	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12471663	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12693557	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12990627	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12992061	0.87[EUR][1000 genomes]
rs13002216	0.85[EUR][1000 genomes]
rs13009889	0.84[EUR][1000 genomes]
rs13011710	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13035966	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1437891	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1550388	0.80[CEU][hapmap];0.80[CHD][hapmap];0.87[JPT][hapmap]
rs1898560	0.80[CEU][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs1899025	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs2017410	0.84[CEU][hapmap]
rs2033746	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs2033870	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs2264018	0.84[CEU][hapmap]
rs2289226	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2289404	0.80[CHD][hapmap]
rs3791767	0.80[CEU][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs3791770	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs3791773	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs3816196	0.85[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs4666783	0.80[CEU][hapmap];0.87[JPT][hapmap]
rs4667296	0.91[ASN][1000 genomes]
rs4667297	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4667299	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5742938	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs5743061	0.85[CEU][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap]
rs5743063	0.85[CEU][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs61487110	0.85[AFR][1000 genomes]
rs6434361	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6434365	0.80[CEU][hapmap];0.87[JPT][hapmap]
rs6719224	0.80[CEU][hapmap]
rs6738042	0.84[EUR][1000 genomes]
rs6741074	0.87[EUR][1000 genomes]
rs6756571	0.83[ASN][1000 genomes]
rs6756913	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6761923	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6942	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs7557519	0.80[CEU][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap]
rs7568449	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7571089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7591929	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs7592066	0.84[EUR][1000 genomes]
rs7595020	0.84[EUR][1000 genomes]
rs893784	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs920427	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs9646811	0.84[CHB][hapmap];0.84[JPT][hapmap];0.82[YRI][hapmap]

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	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:24)

SNP	Gene	Cis/trans	Tissue	Source
rs12693551	ORMDL1	cis	Artery Tibial	GTEx
rs12693551	HIBCH	cis	parietal	SCAN
rs12693551	PMS1	Cis_1M	lymphoblastoid	RTeQTL
rs12693551	ASNSD1	cis	Artery Aorta	GTEx
rs12693551	DIRC1	cis	parietal	SCAN
rs12693551	MFSD6	cis	cerebellum	SCAN
rs12693551	PMS1	cis	cerebellum	SCAN
rs12693551	ORMDL1	cis	cerebellum	SCAN
rs12693551	ORMDL1	cis	lymphoblastoid	seeQTL
rs12693551	ASNSD1	Cis_1M	lymphoblastoid	RTeQTL
rs12693551	ASNSD1	cis	Whole Blood	GTEx
rs12693551	ASNSD1	cis	parietal	SCAN
rs12693551	ORMDL1	Cis_1M	lymphoblastoid	RTeQTL
rs12693551	ORMDL1	cis	parietal	SCAN
rs12693551	ASNSD1	cis	Nerve Tibial	GTEx
rs12693551	ORMDL1	cis	Nerve Tibial	GTEx
rs12693551	ORMDL1	cis	Adipose Subcutaneous	GTEx
rs12693551	ORMDL1	cis	Muscle Skeletal	GTEx
rs12693551	ORMDL1	cis	Skin Sun Exposed Lower leg	GTEx
rs12693551	ASNSD1	cis	Esophagus Muscularis	GTEx
rs12693551	ORMDL1	cis	Heart Left Ventricle	GTEx
rs12693551	ASNSD1	cis	Thyroid	GTEx
rs12693551	PMS1	cis	parietal	SCAN
rs12693551	ASNSD1	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190525600-190529800	Active TSS	GM12878-XiMat	blood
2	chr2:190527000-190534800	Weak transcription	Lung	lung
3	chr2:190527400-190529600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr2:190527400-190529800	Enhancers	Liver	Liver
5	chr2:190527400-190529800	Weak transcription	Fetal Intestine Large	intestine
6	chr2:190527400-190530200	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr2:190527400-190530800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr2:190527400-190530800	Weak transcription	NHLF	lung
9	chr2:190527400-190531200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:190527400-190531600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:190527400-190532000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:190527400-190532200	Weak transcription	Left Ventricle	heart
13	chr2:190527400-190533000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:190527400-190533600	Weak transcription	K562	blood
15	chr2:190527400-190537400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:190527400-190538400	Weak transcription	Pancreas	Pancrea
17	chr2:190527400-190538400	Weak transcription	Right Ventricle	heart
18	chr2:190527400-190538600	Weak transcription	Esophagus	oesophagus
19	chr2:190527400-190538600	Weak transcription	Gastric	stomach
20	chr2:190527400-190539000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr2:190527600-190529400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:190527600-190529600	Enhancers	Colon Smooth Muscle	Colon
23	chr2:190527600-190529800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr2:190527600-190530000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr2:190527600-190530000	Weak transcription	NHDF-Ad	bronchial
26	chr2:190527600-190530400	Weak transcription	Fetal Thymus	thymus
27	chr2:190527600-190530600	Weak transcription	Fetal Kidney	kidney
28	chr2:190527600-190530800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:190527600-190530800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:190527600-190530800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:190527600-190531000	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr2:190527600-190532000	Weak transcription	Aorta	Aorta
33	chr2:190527600-190532600	Weak transcription	Colonic Mucosa	Colon
34	chr2:190527600-190532600	Weak transcription	Fetal Intestine Small	intestine
35	chr2:190527600-190532800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:190527600-190538600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:190527600-190538600	Weak transcription	Spleen	Spleen
38	chr2:190527600-190539200	Weak transcription	Small Intestine	intestine
39	chr2:190527800-190529400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr2:190527800-190529400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr2:190527800-190529400	Enhancers	Fetal Brain Female	brain
42	chr2:190527800-190529400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr2:190527800-190529600	Weak transcription	Primary B cells from peripheral blood	blood
44	chr2:190527800-190529800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:190527800-190529800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr2:190527800-190529800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr2:190527800-190530000	Enhancers	Primary T cells from cord blood	blood
48	chr2:190527800-190530000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr2:190527800-190530000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:190527800-190530200	Enhancers	Primary T helper naive cells from peripheral blood	blood

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