Variant report

Variant	rs893784
Chromosome Location	chr2:190536283-190536284
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:190536047-190539158	K562	blood:	n/a	n/a
2	POLR2A	chr2:190536147-190537247	GM12892	blood:	n/a	n/a
3	POLR2A	chr2:190536215-190536672	GM12878	blood:	n/a	n/a
4	POLR2A	chr2:190536016-190538449	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:190536281-190536489	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:190536283-190536719	GM12891	blood:	n/a	n/a
7	POLR2A	chr2:190536138-190537759	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190308372..190310331-chr2:190535454..190537876,3	MCF-7	breast:

Variant related genes	Relation type
ANKAR	TF binding region

Extended variants
information (count: 75 )
Associated
traits (count: 32 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10195109	0.85[CEU][hapmap];0.87[JPT][hapmap]
rs10197331	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10207346	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10210345	0.95[CEU][hapmap];0.82[ASN][1000 genomes]
rs1055091	0.91[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10931430	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10931431	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10931433	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1132360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11679767	0.91[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11685425	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1225101	0.83[CEU][hapmap];0.91[JPT][hapmap]
rs1233245	0.89[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap]
rs1233262	0.86[EUR][1000 genomes]
rs1233265	0.86[EUR][1000 genomes]
rs1233272	0.85[EUR][1000 genomes]
rs1233282	0.85[EUR][1000 genomes]
rs1233284	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs1233288	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs1233291	0.84[EUR][1000 genomes]
rs1233297	0.90[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs1233299	0.85[EUR][1000 genomes]
rs1233302	1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs1234834	0.84[EUR][1000 genomes]
rs12471217	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12471663	0.82[ASN][1000 genomes]
rs12693551	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]
rs12693557	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12990627	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12992061	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13002216	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13009889	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13011710	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13026135	0.82[EUR][1000 genomes]
rs13035966	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1437891	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1550388	0.85[CEU][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap]
rs1898560	0.85[CEU][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs1899025	0.91[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2017410	0.89[CEU][hapmap]
rs2033746	0.95[CEU][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2033870	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2264018	0.84[CEU][hapmap]
rs2289226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3791767	0.85[CEU][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs3791770	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs3791773	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs3816196	0.91[ASW][hapmap];0.90[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4525728	0.80[EUR][1000 genomes]
rs4666783	0.85[CEU][hapmap];0.87[JPT][hapmap]
rs4667296	0.89[ASN][1000 genomes]
rs4667297	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4667299	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5742933	0.84[CEU][hapmap]
rs5742938	0.91[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs5743061	0.90[CEU][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap]
rs5743063	0.90[CEU][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs6434361	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6434365	0.85[CEU][hapmap];0.87[JPT][hapmap]
rs6719224	0.85[CEU][hapmap]
rs6738042	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6741074	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6756571	0.82[ASN][1000 genomes]
rs6756913	0.82[ASN][1000 genomes]
rs6761923	0.81[ASN][1000 genomes]
rs6942	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7557519	0.85[CEU][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap]
rs7568449	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.90[ASN][1000 genomes]
rs7571089	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7591929	0.91[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs7592066	0.86[EUR][1000 genomes]
rs7595020	0.86[EUR][1000 genomes]
rs920427	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs9646811	0.84[CHB][hapmap];0.84[JPT][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:32)

SNP	Gene	Cis/trans	Tissue	Source
rs893784	ASNSD1	cis	Thyroid	GTEx
rs893784	ORMDL1	cis	multi-tissue	Pritchard
rs893784	ASNSD1	cis	parietal	SCAN
rs893784	LOC51240	cis	multi-tissue	Pritchard
rs893784	HIBCH	cis	parietal	SCAN
rs893784	ORMDL1	Cis_1M	lymphoblastoid	RTeQTL
rs893784	ORMDL1	cis	lesional skin	skin_eQTL
rs893784	ASNSD1	Cis_1M	lymphoblastoid	RTeQTL
rs893784	ORMDL1	cis	Heart Left Ventricle	GTEx
rs893784	ORMDL1	cis	Muscle Skeletal	GTEx
rs893784	ORMDL1	cis	normal skin	skin_eQTL
rs893784	ORMDL1	cis	Adipose Subcutaneous	GTEx
rs893784	ASNSD1	cis	cerebellum	SCAN
rs893784	PMS1	Cis_1M	lymphoblastoid	RTeQTL
rs893784	ORMDL1	cis	Lymphoblastoid	GTEx
rs893784	ASNSD1	cis	Whole Blood	GTEx
rs893784	ASNSD1	cis	uninvolved skin	skin_eQTL
rs893784	MFSD6	cis	cerebellum	SCAN
rs893784	ORMDL1	cis	parietal	SCAN
rs893784	NBLA00058	cis	multi-tissue	Pritchard
rs893784	ASNSD1	cis	Nerve Tibial	GTEx
rs893784	ASNSD1	cis	Artery Tibial	GTEx
rs893784	ORMDL1	cis	cerebellum	SCAN
rs893784	PMS1	cis	parietal	SCAN
rs893784	DIRC1	cis	parietal	SCAN
rs893784	ASNSD1	cis	Artery Aorta	GTEx
rs893784	ORMDL1	cis	uninvolved skin	skin_eQTL
rs893784	PMS1	cis	cerebellum	SCAN
rs893784	ORMDL1	cis	lymphoblastoid	seeQTL
rs893784	ASNSD1	cis	Esophagus Muscularis	GTEx
rs893784	ORMDL1	cis	Artery Tibial	GTEx
rs893784	ORMDL1	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190527400-190537400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr2:190527400-190538400	Weak transcription	Pancreas	Pancrea
3	chr2:190527400-190538400	Weak transcription	Right Ventricle	heart
4	chr2:190527400-190538600	Weak transcription	Esophagus	oesophagus
5	chr2:190527400-190538600	Weak transcription	Gastric	stomach
6	chr2:190527400-190539000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:190527600-190538600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:190527600-190538600	Weak transcription	Spleen	Spleen
9	chr2:190527600-190539200	Weak transcription	Small Intestine	intestine
10	chr2:190527800-190538400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:190527800-190538400	Weak transcription	Psoas Muscle	Psoas
12	chr2:190527800-190538600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:190528200-190537600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:190528200-190541600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:190528400-190537400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr2:190528600-190538000	Weak transcription	Fetal Heart	heart
17	chr2:190528600-190539600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:190528800-190537000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:190529000-190537000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:190529000-190537200	Strong transcription	Placenta	Placenta
21	chr2:190529000-190537800	Strong transcription	HSMM	muscle
22	chr2:190529200-190537200	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr2:190529400-190537200	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr2:190529600-190537000	Strong transcription	Primary B cells from peripheral blood	blood
25	chr2:190529600-190537200	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:190529800-190537200	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr2:190529800-190537200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:190529800-190537200	Strong transcription	Fetal Intestine Large	intestine
29	chr2:190529800-190537600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr2:190530000-190537000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:190530000-190537600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr2:190530000-190542800	Strong transcription	Dnd41	blood
33	chr2:190530200-190537000	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr2:190530400-190536800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:190530400-190537200	Strong transcription	Duodenum Mucosa	Duodenum
36	chr2:190530400-190537200	Strong transcription	NH-A	brain
37	chr2:190530400-190537800	Strong transcription	Fetal Thymus	thymus
38	chr2:190530400-190538200	Strong transcription	Fetal Muscle Leg	muscle
39	chr2:190530600-190536800	Strong transcription	Osteobl	bone
40	chr2:190530600-190537200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr2:190530600-190537400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr2:190530600-190537400	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr2:190530800-190537000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr2:190530800-190537000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:190530800-190537000	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr2:190530800-190537200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:190530800-190537200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:190530800-190537200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr2:190531000-190537000	Strong transcription	Fetal Muscle Trunk	muscle
50	chr2:190531000-190537200	Strong transcription	HUES6 Cell Line	embryonic stem cell

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