Variant report

Variant	rs2793812
Chromosome Location	chr1:179159399-179159400
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179157213..179159659-chr1:179198340..179199945,2	MCF-7	breast:
2	chr1:179157109..179159838-chr1:179172686..179174589,2	K562	blood:

Variant related genes	Relation type
ENSG00000143322	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs1078872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10913690	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.92[EUR][1000 genomes]
rs10913692	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs10913695	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10913697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1173077	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs12130276	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs1325194	0.86[GIH][hapmap]
rs1325195	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1763022	0.86[ASN][1000 genomes]
rs1807916	0.85[ASN][1000 genomes]
rs1826183	0.93[ASN][1000 genomes]
rs1856967	0.93[EUR][1000 genomes]
rs1856968	0.92[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1858551	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2050923	0.86[ASN][1000 genomes]
rs2066279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2087559	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2130576	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2171958	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2171959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2258217	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2258221	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2306941	0.83[ASN][1000 genomes]
rs2486995	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2486997	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2487563	0.86[ASN][1000 genomes]
rs2493124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2636265	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2636266	0.85[GIH][hapmap];0.80[TSI][hapmap]
rs2636272	0.86[ASN][1000 genomes]
rs2636274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2636276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2636277	0.95[CHB][hapmap];1.00[CHD][hapmap]
rs2636280	0.92[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];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2636281	0.94[EUR][1000 genomes]
rs2636282	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2636287	0.96[CEU][hapmap];0.81[JPT][hapmap];0.95[EUR][1000 genomes]
rs2636290	0.90[GIH][hapmap]
rs2636293	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2791936	0.81[ASN][1000 genomes]
rs2791940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2791941	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2791942	0.85[EUR][1000 genomes]
rs2791943	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2791944	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2791945	0.84[ASN][1000 genomes]
rs2793790	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2793793	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2793795	0.89[EUR][1000 genomes]
rs2793796	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2793797	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.81[AFR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2793798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2793799	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs2793801	0.85[ASN][1000 genomes]
rs2793802	0.87[ASN][1000 genomes]
rs2793803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2793805	0.85[GIH][hapmap]
rs2793806	0.93[EUR][1000 genomes]
rs2793810	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs2793813	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs2793816	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs2816166	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2816167	0.94[EUR][1000 genomes]
rs2816168	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2816183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2816184	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2816185	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2816186	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2816187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2816189	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2816190	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2816191	0.86[ASN][1000 genomes]
rs2816193	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2816196	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2816197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2816198	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2816199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2816200	0.90[ASN][1000 genomes]
rs2816201	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2816202	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2816203	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2816204	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2816206	0.95[EUR][1000 genomes]
rs2816207	0.88[ASN][1000 genomes]
rs2816208	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2816209	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs2816210	0.92[EUR][1000 genomes]
rs2816211	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2816212	0.84[ASN][1000 genomes]
rs2816213	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap]
rs2816214	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2816218	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs3121198	0.81[ASN][1000 genomes]
rs3122376	0.91[ASN][1000 genomes]
rs3210839	0.96[CEU][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs36122838	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs377785	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3813642	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3813643	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3818433	0.90[GIH][hapmap]
rs3829794	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs411266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs413613	0.84[ASN][1000 genomes]
rs434283	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs451088	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4651012	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4651013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6668200	0.83[LWK][hapmap];1.00[YRI][hapmap]
rs7556011	0.83[EUR][1000 genomes]
rs915337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9425839	0.88[ASN][1000 genomes]
rs965401	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9662858	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs9726961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9727252	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9728480	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9729199	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2793812	TOR3A	cis	Artery Tibial	GTEx
rs2793812	IER5	cis	cerebellum	SCAN
rs2793812	FAM20B	cis	parietal	SCAN
rs2793812	FAM20B	cis	lymphoblastoid	seeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179117800-179186000	Weak transcription	Fetal Stomach	stomach
2	chr1:179122000-179189400	Weak transcription	Primary B cells from cord blood	blood
3	chr1:179134000-179169000	Weak transcription	Fetal Intestine Small	intestine
4	chr1:179139400-179196800	Weak transcription	Pancreas	Pancrea
5	chr1:179145000-179159800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:179145000-179159800	Weak transcription	Brain Angular Gyrus	brain
7	chr1:179146800-179175600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:179147600-179160000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr1:179147600-179174600	Weak transcription	Psoas Muscle	Psoas
10	chr1:179148000-179186000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:179148400-179185800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:179150600-179176000	Weak transcription	HSMM	muscle
13	chr1:179150800-179170600	Weak transcription	Ovary	ovary
14	chr1:179150800-179178000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:179150800-179180400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:179153600-179160000	Weak transcription	GM12878-XiMat	blood
17	chr1:179153600-179169800	Weak transcription	Small Intestine	intestine
18	chr1:179154000-179171600	Weak transcription	Primary T cells from cord blood	blood
19	chr1:179154200-179159400	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr1:179154400-179159800	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr1:179155600-179160200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:179156400-179169200	Weak transcription	Fetal Intestine Large	intestine
23	chr1:179156400-179177800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:179156800-179171400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr1:179157400-179159800	Weak transcription	Osteobl	bone
26	chr1:179157400-179164200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:179157400-179197400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:179157400-179197600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:179157600-179170600	Weak transcription	Lung	lung
30	chr1:179157600-179177800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:179157800-179159800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:179158000-179160000	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr1:179158600-179159400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:179158600-179159600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:179158800-179160000	Weak transcription	K562	blood
36	chr1:179159000-179159800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr1:179159200-179160400	Enhancers	iPS-15b Cell Line	embryonic stem cell

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