Variant report

Variant	rs524492
Chromosome Location	chr6:44796596-44796597
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:44794819..44797598-chr6:44800696..44803028,2	K562	blood:

Extended variants
information (count: 125 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs1023091	0.88[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs1028944	0.88[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap]
rs10484627	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs10948185	0.89[CHD][hapmap]
rs10948187	0.87[CHD][hapmap]
rs10948188	0.86[CHD][hapmap]
rs10948190	0.87[CHD][hapmap]
rs10948194	0.87[CHD][hapmap]
rs10948197	0.87[CHD][hapmap]
rs1159131	0.84[CHD][hapmap]
rs12196818	0.84[CHD][hapmap]
rs12214778	0.87[CHD][hapmap]
rs12525773	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12526711	0.83[JPT][hapmap]
rs12526755	0.84[ASN][1000 genomes]
rs12527908	0.87[ASN][1000 genomes]
rs12528232	0.88[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs12529522	0.82[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs12530016	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]
rs12661902	0.82[ASN][1000 genomes]
rs12663530	0.85[ASN][1000 genomes]
rs12663798	0.84[ASN][1000 genomes]
rs13202672	0.96[ASN][1000 genomes]
rs13206526	0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs13215618	0.84[CHB][hapmap]
rs13216116	0.87[CHD][hapmap]
rs13216967	0.82[ASN][1000 genomes]
rs1329710	0.87[CHD][hapmap]
rs1329715	0.88[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs1329716	0.89[CHD][hapmap]
rs1360195	0.88[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs1402599	1.00[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];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1418435	0.83[ASN][1000 genomes]
rs16869119	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16872574	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17422760	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs1935549	0.97[ASN][1000 genomes]
rs1980265	0.87[CHD][hapmap]
rs2139863	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs227852	0.84[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap]
rs227853	0.84[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap]
rs227857	0.82[ASN][1000 genomes]
rs2396369	0.87[CHD][hapmap]
rs2396371	0.84[CHB][hapmap];0.84[YRI][hapmap]
rs2396372	0.89[CHD][hapmap]
rs2894599	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs34243039	0.93[ASN][1000 genomes]
rs34286542	0.83[ASN][1000 genomes]
rs34776198	0.96[ASN][1000 genomes]
rs34817919	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35103634	0.84[ASN][1000 genomes]
rs35687006	0.88[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs35704584	0.84[ASN][1000 genomes]
rs35856781	0.93[ASN][1000 genomes]
rs35908738	0.83[ASN][1000 genomes]
rs36105034	0.83[ASN][1000 genomes]
rs3778507	0.87[CHD][hapmap]
rs3799965	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3799966	0.96[ASN][1000 genomes]
rs3799967	0.88[JPT][hapmap]
rs3799969	0.96[ASN][1000 genomes]
rs3799970	0.96[ASN][1000 genomes]
rs3799971	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs3799972	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3799973	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs3799974	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3799976	0.83[JPT][hapmap]
rs3799977	0.87[CHD][hapmap];0.83[JPT][hapmap]
rs3799979	0.87[CHD][hapmap];0.83[JPT][hapmap]
rs3799984	0.83[JPT][hapmap]
rs3799986	0.87[CHD][hapmap]
rs3799987	0.88[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs3823252	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3997503	0.84[ASN][1000 genomes]
rs4475320	0.84[ASN][1000 genomes]
rs4512220	0.88[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs4711809	0.82[CHB][hapmap];0.89[CHD][hapmap];0.81[ASN][1000 genomes]
rs4714812	0.94[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs4714825	0.97[ASN][1000 genomes]
rs4714827	0.93[ASN][1000 genomes]
rs4714828	0.87[CHD][hapmap];0.83[JPT][hapmap]
rs4714829	0.84[ASN][1000 genomes]
rs4714830	0.87[CHD][hapmap]
rs4714834	0.88[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs494982	0.86[CHD][hapmap]
rs542444	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs562016	0.97[ASN][1000 genomes]
rs59945128	0.84[ASN][1000 genomes]
rs608941	0.87[CHD][hapmap]
rs609643	0.82[ASN][1000 genomes]
rs609699	0.82[ASN][1000 genomes]
rs636845	0.87[CHD][hapmap];0.84[YRI][hapmap]
rs66642874	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs67597621	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs67911131	0.86[ASN][1000 genomes]
rs6904015	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs6904584	0.87[ASN][1000 genomes]
rs6910294	0.83[JPT][hapmap]
rs6919161	0.88[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs720988	0.96[ASN][1000 genomes]
rs720989	0.94[ASN][1000 genomes]
rs72664272	0.94[ASN][1000 genomes]
rs72664273	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72664274	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7746032	0.84[ASN][1000 genomes]
rs7754378	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs7754698	0.86[JPT][hapmap]
rs7769218	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9296450	0.94[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9357464	0.84[YRI][hapmap]
rs9367211	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs9369514	0.83[JPT][hapmap]
rs9369516	0.87[CHD][hapmap];0.83[JPT][hapmap]
rs9395051	0.87[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs9463017	0.83[ASN][1000 genomes]
rs9463039	0.93[ASN][1000 genomes]
rs9463040	0.93[ASN][1000 genomes]
rs9472331	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs9472335	0.83[ASN][1000 genomes]
rs9472376	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9472407	0.82[JPT][hapmap]
rs9472409	0.87[CHD][hapmap]
rs9472414	0.94[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9885796	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]

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	esv1842105	chr6:44783457-44798701	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs524492	CD2AP	cis	cerebellum	SCAN
rs524492	SUPT3H	cis	lymphoblastoid	seeQTL
rs524492	SUPT3H	cis	multi-tissue	Pritchard
rs524492	PRPH2	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44777400-44796600	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr6:44779600-44796600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr6:44779600-44796800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr6:44779600-44796800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:44780000-44798400	Weak transcription	Dnd41	blood
6	chr6:44785200-44796800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr6:44786200-44797200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr6:44789200-44796800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr6:44790400-44797200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:44791000-44805600	Weak transcription	Ovary	ovary
11	chr6:44791200-44799000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:44792000-44811600	Weak transcription	Pancreas	Pancrea
13	chr6:44792200-44796600	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr6:44792400-44796800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:44792800-44796600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr6:44792800-44796800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr6:44792800-44797000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr6:44792800-44797200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr6:44793400-44797200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr6:44793400-44798000	Weak transcription	HepG2	liver
21	chr6:44793600-44796600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr6:44793800-44797400	Weak transcription	Fetal Intestine Large	intestine
23	chr6:44794200-44796800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr6:44794600-44798200	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr6:44795000-44796800	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr6:44795600-44798200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:44795800-44798000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr6:44796200-44798200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:44796200-44798200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:44796200-44798400	Enhancers	Primary T cells from cord blood	blood
31	chr6:44796200-44798400	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr6:44796400-44797600	Enhancers	Primary hematopoietic stem cells	blood
33	chr6:44796400-44797600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:44796400-44798000	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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