Variant report

Variant	rs6504108
Chromosome Location	chr17:46292923-46292924
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46292574..46293563-chr17:46384878..46385708,4	MCF-7	breast:
2	chr17:46292856..46293447-chr17:46385046..46385772,2	MCF-7	breast:
3	chr17:46292783..46295645-chr17:46342921..46345128,2	K562	blood:
4	chr17:46286598..46289280-chr17:46291175..46294782,3	K562	blood:
5	chr17:46292744..46293326-chr17:46451926..46452607,2	MCF-7	breast:
6	chr17:46292724..46293589-chr17:46413037..46413890,2	MCF-7	breast:
7	chr17:46292623..46293264-chr17:46337039..46337586,2	MCF-7	breast:
8	chr17:46292649..46293615-chr17:46326688..46327277,2	K562	blood:
9	chr17:46292653..46293618-chr17:46336496..46337643,9	MCF-7	breast:
10	chr17:46292663..46294856-chr17:46339280..46340993,2	MCF-7	breast:
11	chr17:46292707..46293506-chr17:46670895..46671869,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000120075	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs1002330	0.96[ASN][1000 genomes]
rs1010228	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs10445339	0.95[ASN][1000 genomes]
rs10445377	0.96[ASN][1000 genomes]
rs10853098	0.96[ASN][1000 genomes]
rs11079806	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs11079808	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs11079814	0.98[ASN][1000 genomes]
rs11651097	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs11870056	0.91[ASN][1000 genomes]
rs11872095	0.98[ASN][1000 genomes]
rs12150533	1.00[ASN][1000 genomes]
rs12452956	0.98[ASN][1000 genomes]
rs12603115	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs12936369	0.82[ASN][1000 genomes]
rs12936731	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs12941830	0.96[ASN][1000 genomes]
rs12947089	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12948810	0.81[ASN][1000 genomes]
rs1316657	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1377201	0.92[ASN][1000 genomes]
rs1452662	0.84[ASN][1000 genomes]
rs1452663	0.84[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs1452665	0.85[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs1452666	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1452667	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1468270	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs16951519	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs16953927	0.84[ASN][1000 genomes]
rs16953941	0.85[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs16954268	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs16954324	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs17620033	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17681336	0.96[ASN][1000 genomes]
rs1860862	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs1860863	0.92[ASN][1000 genomes]
rs1979897	0.85[CHB][hapmap]
rs2021752	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2021811	0.95[ASN][1000 genomes]
rs2041572	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs2051821	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2060876	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2072441	0.81[CHB][hapmap]
rs208005	0.85[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs208008	0.85[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs208009	0.85[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs208011	0.82[ASN][1000 genomes]
rs208012	0.82[ASN][1000 genomes]
rs208015	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs208019	0.80[ASN][1000 genomes]
rs2109982	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2109983	0.80[JPT][hapmap]
rs2109984	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2123341	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2229369	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2240120	0.85[CHB][hapmap]
rs2240121	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2240122	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2278868	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2305433	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2325804	0.85[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs2325885	0.84[ASN][1000 genomes]
rs2924257	0.86[CHB][hapmap]
rs2938483	0.92[ASN][1000 genomes]
rs34949267	0.96[ASN][1000 genomes]
rs34980108	0.84[ASN][1000 genomes]
rs36071506	0.84[ASN][1000 genomes]
rs3744346	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs3792692	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3792694	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3805363	0.93[ASN][1000 genomes]
rs3805370	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3805371	0.98[ASN][1000 genomes]
rs3815472	0.80[ASN][1000 genomes]
rs3897986	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3944039	0.92[ASN][1000 genomes]
rs4793779	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs4794447	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4794451	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs4794505	1.00[ASN][1000 genomes]
rs4794517	1.00[ASN][1000 genomes]
rs4794525	0.98[ASN][1000 genomes]
rs55696440	0.82[ASN][1000 genomes]
rs55982346	1.00[ASN][1000 genomes]
rs62066407	0.81[ASN][1000 genomes]
rs62066447	1.00[ASN][1000 genomes]
rs6504025	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs6847	0.81[JPT][hapmap]
rs7210149	1.00[ASN][1000 genomes]
rs7212202	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs7213876	0.98[ASN][1000 genomes]
rs7217496	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs7219967	1.00[ASN][1000 genomes]
rs7220619	0.87[ASN][1000 genomes]
rs7220768	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7220922	0.96[ASN][1000 genomes]
rs7222136	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs7223867	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7224014	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs7225435	0.91[ASN][1000 genomes]
rs7225550	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7225865	0.94[ASN][1000 genomes]
rs7501770	0.92[ASN][1000 genomes]
rs758999	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs8065670	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs8066391	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs8069064	1.00[ASN][1000 genomes]
rs8069263	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8071199	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs8071879	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs8072282	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8075270	0.98[ASN][1000 genomes]
rs8077860	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs8079616	0.80[ASN][1000 genomes]
rs875065	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs882380	1.00[ASN][1000 genomes]
rs954226	0.89[ASN][1000 genomes]
rs978263	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs9899275	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs9899461	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs9903692	0.82[ASN][1000 genomes]
rs9909933	0.84[ASN][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6504108	CDK5RAP3	cis	cerebellum	SCAN
rs6504108	DHX58	cis	parietal	SCAN
rs6504108	ASB16	cis	parietal	SCAN
rs6504108	AARSD1	cis	parietal	SCAN
rs6504108	CDK5RAP3	cis	parietal	SCAN
rs6504108	CDK5RAP3	cis	Thyroid	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46266800-46298600	Weak transcription	Thymus	Thymus
2	chr17:46266800-46318200	Weak transcription	Primary B cells from peripheral blood	blood
3	chr17:46273200-46293000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr17:46273200-46302800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr17:46273200-46314000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr17:46274200-46297200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr17:46280000-46295800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr17:46283600-46314000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr17:46286800-46297400	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr17:46287800-46293200	Weak transcription	GM12878-XiMat	blood
11	chr17:46288400-46307000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr17:46289600-46294600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr17:46290200-46293000	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr17:46291600-46294200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr17:46292000-46294600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr17:46292600-46294000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr17:46292600-46295200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr17:46292800-46293600	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr17:46292800-46293600	Enhancers	K562	blood
20	chr17:46292800-46293800	Enhancers	A549	lung
21	chr17:46292800-46296000	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr17:46292800-46298600	Strong transcription	Primary T cells from cord blood	blood

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