Variant report

Variant	rs2290717
Chromosome Location	chr12:10783729-10783730
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:10766041..10767733-chr12:10782838..10785300,2	MCF-7	breast:
2	chr12:10783181..10785350-chr12:10788127..10790504,2	K562	blood:
3	chr12:10782687..10785375-chr12:10794891..10797220,2	MCF-7	breast:
4	chr12:10782352..10785232-chr12:10787939..10791326,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111196	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10431297	0.96[CEU][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs1073305	0.96[CEU][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs10772339	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10772340	0.96[CEU][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs10772343	0.91[CEU][hapmap];0.85[JPT][hapmap]
rs10772347	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs1078437	0.84[CEU][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs10845186	0.91[ASN][1000 genomes]
rs10845187	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845188	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845189	0.83[EUR][1000 genomes]
rs10845192	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs10845194	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs10845195	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs10845197	0.96[CEU][hapmap]
rs10845198	0.86[JPT][hapmap]
rs11053886	0.88[ASN][1000 genomes]
rs12316690	0.95[CEU][hapmap]
rs12321017	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12582745	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17742332	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1979268	1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[ASN][1000 genomes]
rs1993498	0.84[CEU][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.85[TSI][hapmap]
rs1993500	0.87[ASN][1000 genomes]
rs2009908	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2054194	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2054195	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2168746	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2168747	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2168748	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2252664	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2277410	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2418087	0.96[CEU][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs2418088	0.96[CEU][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs2418095	0.95[CEU][hapmap]
rs2900513	0.90[CEU][hapmap];0.86[JPT][hapmap]
rs3759259	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3759260	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3782671	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3983439	0.86[EUR][1000 genomes]
rs4763573	0.96[CEU][hapmap]
rs61912160	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61912161	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61912180	0.81[EUR][1000 genomes]
rs6488316	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs7313620	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs7350557	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs7350597	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs7968284	0.86[JPT][hapmap]
rs7970568	0.96[CEU][hapmap]
rs7971142	0.96[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs8181761	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][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	nsv832329	chr12:10677094-10845946	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv607	chr12:10776867-10821535	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2290717	TPI1	cis	parietal	SCAN
rs2290717	TAS2R31	cis	cerebellum	SCAN
rs2290717	TAS2R19	cis	cerebellum	SCAN
rs2290717	TAS2R14	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10766600-10787000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:10766600-10789400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:10766600-10794400	Weak transcription	Gastric	stomach
4	chr12:10766800-10789400	Weak transcription	Esophagus	oesophagus
5	chr12:10772000-10787200	Weak transcription	NHEK	skin
6	chr12:10773000-10786600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr12:10773000-10787000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:10773400-10787000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:10774600-10784000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr12:10774600-10784400	Weak transcription	HSMMtube	muscle
11	chr12:10776200-10784200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:10776200-10785200	Weak transcription	HSMM	muscle
13	chr12:10777600-10784000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr12:10777600-10786600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr12:10777600-10787400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:10777800-10786400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:10779800-10790000	Strong transcription	HUVEC	blood vessel
18	chr12:10781000-10784200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:10781000-10786400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr12:10781000-10787000	Weak transcription	HMEC	breast
21	chr12:10781800-10786200	Weak transcription	Stomach Mucosa	stomach
22	chr12:10782200-10787600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:10782200-10791000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:10782400-10789400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr12:10783600-10784200	Strong transcription	Rectal Mucosa Donor 31	rectum

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