Variant report

Variant	rs12530016
Chromosome Location	chr6:44866322-44866323
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	TCF12	chr6:44866236-44866626	H1-hESC	embryonic stem cell:	n/a	chr6:44866476-44866483 chr6:44866455-44866462
2	TEAD4	chr6:44866164-44866485	H1-hESC	embryonic stem cell:	n/a	n/a
3	TEAD4	chr6:44865978-44866536	ECC-1	luminal epithelium:	n/a	n/a
4	TEAD4	chr6:44866027-44866555	ECC-1	luminal epithelium:	n/a	n/a
5	TCF12	chr6:44865910-44866570	ECC-1	luminal epithelium:	n/a	chr6:44866476-44866483 chr6:44866455-44866462

Variant related genes	Relation type
NUDT19P4	TF binding region

Extended variants
information (count: 213 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:210)

rs_ID	r²[population]
rs1023090	0.84[JPT][hapmap]
rs1023091	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1028944	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs1041332	0.84[JPT][hapmap]
rs10456119	0.84[ASN][1000 genomes]
rs10484627	0.89[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs10948183	0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs10948185	0.89[CHD][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs10948186	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs10948187	0.87[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs10948188	0.86[CHD][hapmap];0.87[YRI][hapmap];0.82[ASN][1000 genomes]
rs10948190	0.87[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs10948193	0.81[ASN][1000 genomes]
rs10948194	0.87[CHD][hapmap];0.81[ASN][1000 genomes]
rs10948197	0.87[CHD][hapmap];0.80[ASN][1000 genomes]
rs10948198	0.84[JPT][hapmap]
rs1159131	0.84[CHD][hapmap];0.91[YRI][hapmap]
rs11964325	0.83[JPT][hapmap]
rs11966936	0.84[JPT][hapmap]
rs11967188	0.81[ASN][1000 genomes]
rs12190513	0.83[JPT][hapmap];0.88[YRI][hapmap];0.82[ASN][1000 genomes]
rs12191518	0.82[ASN][1000 genomes]
rs12196818	0.84[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs12198904	0.83[ASN][1000 genomes]
rs12205071	0.84[JPT][hapmap]
rs12207620	0.83[ASN][1000 genomes]
rs12208023	0.84[JPT][hapmap]
rs12209076	0.83[ASN][1000 genomes]
rs12214778	0.87[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs12524069	0.81[ASN][1000 genomes]
rs12525009	0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs12525773	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12526649	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs12526711	0.88[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs12526755	0.94[ASN][1000 genomes]
rs12527908	0.97[ASN][1000 genomes]
rs12528232	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12528762	0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs12529490	0.84[JPT][hapmap]
rs12529522	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12529990	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs12661902	0.92[ASN][1000 genomes]
rs12663530	0.97[ASN][1000 genomes]
rs12663798	0.94[ASN][1000 genomes]
rs1284986	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs1284987	0.84[JPT][hapmap]
rs1284988	0.84[JPT][hapmap]
rs1293598	0.85[ASN][1000 genomes]
rs13196587	0.83[ASN][1000 genomes]
rs13201942	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs13202672	0.89[ASN][1000 genomes]
rs13203495	0.81[ASN][1000 genomes]
rs13205113	0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs13206526	0.92[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs13209827	0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs13211006	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs13211229	0.82[ASN][1000 genomes]
rs13213412	0.82[ASN][1000 genomes]
rs13215618	0.84[JPT][hapmap]
rs13216116	0.87[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs13216967	0.94[ASN][1000 genomes]
rs1329710	0.87[CHD][hapmap]
rs1329713	0.87[CHD][hapmap];0.84[JPT][hapmap]
rs1329714	0.81[JPT][hapmap]
rs1329715	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1329716	0.89[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs1360195	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1402599	0.82[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1411148	0.84[JPT][hapmap]
rs1521355	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs1576382	0.81[ASN][1000 genomes]
rs1578676	0.81[ASN][1000 genomes]
rs1590864	0.82[ASN][1000 genomes]
rs16869119	0.92[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs16872574	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17339124	0.83[ASN][1000 genomes]
rs17422760	0.89[CHD][hapmap];0.89[JPT][hapmap];0.88[YRI][hapmap];0.85[ASN][1000 genomes]
rs17424547	0.84[JPT][hapmap]
rs1854547	0.82[ASN][1000 genomes]
rs1935549	0.87[ASN][1000 genomes]
rs1937046	0.84[JPT][hapmap]
rs1971482	0.84[JPT][hapmap]
rs1980265	0.87[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2139863	0.87[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2186062	0.84[JPT][hapmap]
rs227852	0.88[CHB][hapmap]
rs227853	0.88[CHB][hapmap]
rs2396369	0.87[CHD][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs2396370	0.82[ASN][1000 genomes]
rs2396371	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs2396372	0.89[CHD][hapmap];0.81[ASN][1000 genomes]
rs2894599	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs34243039	0.91[ASN][1000 genomes]
rs34286542	0.93[ASN][1000 genomes]
rs34776198	0.88[ASN][1000 genomes]
rs34808716	0.84[ASN][1000 genomes]
rs34817919	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35103634	0.94[ASN][1000 genomes]
rs35357222	0.82[ASN][1000 genomes]
rs35687006	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs35704584	0.94[ASN][1000 genomes]
rs35813980	0.81[ASN][1000 genomes]
rs35856781	0.91[ASN][1000 genomes]
rs35908738	0.93[ASN][1000 genomes]
rs36105034	0.93[ASN][1000 genomes]
rs3778507	0.87[CHD][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs3799965	0.88[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs3799966	0.87[ASN][1000 genomes]
rs3799967	0.81[JPT][hapmap]
rs3799969	0.88[ASN][1000 genomes]
rs3799970	0.88[ASN][1000 genomes]
rs3799971	0.82[JPT][hapmap]
rs3799972	0.92[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs3799973	0.81[JPT][hapmap]
rs3799974	0.92[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs3799976	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs3799977	0.87[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs3799979	0.87[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs3799981	0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs3799984	0.89[JPT][hapmap];0.88[YRI][hapmap];0.81[ASN][1000 genomes]
rs3799986	0.87[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs3799987	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs3823252	0.92[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs3846896	0.83[ASN][1000 genomes]
rs3957281	0.86[ASN][1000 genomes]
rs4398713	0.87[CHD][hapmap];0.84[JPT][hapmap]
rs4412189	0.84[JPT][hapmap]
rs4475320	0.94[ASN][1000 genomes]
rs4512220	0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs4711803	0.86[ASN][1000 genomes]
rs4711805	0.86[ASN][1000 genomes]
rs4711807	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs4711809	0.88[CHB][hapmap];0.89[CHD][hapmap];0.91[ASN][1000 genomes]
rs4714812	0.88[CHB][hapmap]
rs4714825	0.87[ASN][1000 genomes]
rs4714827	0.91[ASN][1000 genomes]
rs4714828	0.87[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4714829	0.94[ASN][1000 genomes]
rs4714830	0.87[CHD][hapmap];0.81[ASN][1000 genomes]
rs4714834	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4714836	0.84[JPT][hapmap]
rs472672	0.80[ASN][1000 genomes]
rs472673	0.81[ASN][1000 genomes]
rs494982	0.86[CHD][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs500773	0.84[ASN][1000 genomes]
rs524492	0.83[ASW][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs538801	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs542444	0.88[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs55893720	0.81[ASN][1000 genomes]
rs562016	0.87[ASN][1000 genomes]
rs588848	0.82[ASN][1000 genomes]
rs59945128	0.94[ASN][1000 genomes]
rs608941	0.87[CHD][hapmap];0.83[ASN][1000 genomes]
rs62438007	0.84[ASN][1000 genomes]
rs636845	0.87[CHD][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs6458414	0.84[ASN][1000 genomes]
rs6458415	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs66642874	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs67597621	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs67911131	0.96[ASN][1000 genomes]
rs679713	0.81[ASN][1000 genomes]
rs6899845	0.84[JPT][hapmap]
rs6903576	0.83[ASN][1000 genomes]
rs6904015	0.82[JPT][hapmap]
rs6904584	0.97[ASN][1000 genomes]
rs6919161	0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs6919485	0.81[ASN][1000 genomes]
rs6922660	0.84[JPT][hapmap]
rs6922772	0.84[JPT][hapmap]
rs6923519	0.87[ASN][1000 genomes]
rs6925017	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs6925467	0.84[JPT][hapmap]
rs718112	0.87[ASN][1000 genomes]
rs720988	0.88[ASN][1000 genomes]
rs720989	0.86[ASN][1000 genomes]
rs72664272	0.84[ASN][1000 genomes]
rs72664273	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72664274	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7742360	0.84[JPT][hapmap]
rs7745506	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs7747642	0.83[ASN][1000 genomes]
rs7749865	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs7754378	0.86[CHD][hapmap];0.89[JPT][hapmap];0.87[YRI][hapmap];0.87[ASN][1000 genomes]
rs7763421	0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs7763450	0.84[JPT][hapmap]
rs7769218	0.86[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs9296450	0.92[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9357464	0.81[ASN][1000 genomes]
rs9357469	0.84[JPT][hapmap]
rs9357470	0.84[JPT][hapmap]
rs9367211	0.87[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs9367214	0.84[JPT][hapmap]
rs9369516	0.87[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs9369529	0.84[JPT][hapmap]
rs9395051	0.87[CHD][hapmap];0.82[JPT][hapmap]
rs9395055	0.85[ASN][1000 genomes]
rs9463039	0.85[ASN][1000 genomes]
rs9463040	0.85[ASN][1000 genomes]
rs9463054	0.81[ASN][1000 genomes]
rs9463055	0.81[ASN][1000 genomes]
rs9472331	0.87[CHB][hapmap]
rs9472376	0.83[ASW][hapmap];0.86[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9472407	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs9472409	0.87[CHD][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs9472411	0.83[ASN][1000 genomes]
rs9472414	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9472416	0.83[YRI][hapmap];0.81[ASN][1000 genomes]
rs969211	0.84[JPT][hapmap]
rs976699	0.81[ASN][1000 genomes]
rs9885796	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885861	chr6:44837356-45043618	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1033815	chr6:44845514-44938799	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv5286	chr6:44865290-44909915	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12530016	SUPT3H	cis	multi-tissue	Pritchard
rs12530016	AARS2	cis	cerebellum	SCAN
rs12530016	UNC5CL	cis	cerebellum	SCAN
rs12530016	SUPT3H	cis	lymphoblastoid	seeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44859200-44889400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr6:44862600-44889400	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr6:44863200-44866600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr6:44863600-44870400	Weak transcription	Aorta	Aorta
5	chr6:44864000-44866600	Enhancers	Fetal Lung	lung
6	chr6:44864200-44866600	Enhancers	Fetal Stomach	stomach
7	chr6:44864800-44888400	Weak transcription	Primary T cells from cord blood	blood
8	chr6:44866000-44866600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:44866000-44866600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:44866000-44866600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:44866000-44866600	Enhancers	Gastric	stomach
12	chr6:44866000-44866600	Enhancers	HSMMtube	muscle
13	chr6:44866000-44866600	Enhancers	NHDF-Ad	bronchial
14	chr6:44866000-44866600	Enhancers	NHLF	lung
15	chr6:44866200-44866400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr6:44866200-44866600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:44866200-44866600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:44866200-44866600	Enhancers	Placenta	Placenta
19	chr6:44866200-44866600	Enhancers	NH-A	brain
20	chr6:44866200-44866800	Enhancers	HSMM	muscle

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