Variant report

Variant	rs2924250
Chromosome Location	chr17:46343119-46343120
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46342466..46344895-chr17:46702495..46704944,2	MCF-7	breast:
2	chr17:46331179..46335442-chr17:46341781..46344659,3	K562	blood:
3	chr17:46338702..46340433-chr17:46342377..46345030,3	K562	blood:
4	chr17:46320871..46323469-chr17:46343037..46345002,2	K562	blood:
5	chr17:46340880..46343379-chr17:46515799..46517839,2	K562	blood:
6	chr17:46340828..46343787-chr17:46696825..46699589,2	K562	blood:
7	chr17:46292783..46295645-chr17:46342921..46345128,2	K562	blood:

Variant related genes	Relation type
ENSG00000170689	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12603827	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12937347	0.89[ASN][1000 genomes]
rs1396868	0.82[ASN][1000 genomes]
rs1509635	0.81[JPT][hapmap]
rs1553750	0.91[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2123344	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2924254	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2938470	1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4239201	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4324172	0.92[ASN][1000 genomes]
rs4423463	0.94[ASN][1000 genomes]
rs4606751	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4793816	0.88[ASN][1000 genomes]
rs6504115	0.81[YRI][hapmap]
rs6504160	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6504210	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7211099	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7211780	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs7213149	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7216202	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7218287	0.80[ASN][1000 genomes]
rs7218563	0.94[ASN][1000 genomes]
rs7221510	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs8072002	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs8077516	0.91[ASN][1000 genomes]
rs8077763	0.89[ASN][1000 genomes]
rs9303541	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs9797269	0.86[ASN][1000 genomes]
rs9898383	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs9906658	0.88[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2924250	CDK5RAP3	cis	cerebellum	SCAN
rs2924250	CDK5RAP3	cis	parietal	SCAN
rs2924250	CCR10	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46319600-46372000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr17:46322800-46356200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr17:46323000-46370800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr17:46324200-46355800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr17:46324200-46371600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr17:46326200-46361200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr17:46339200-46343400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr17:46339400-46343600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr17:46339600-46343800	Enhancers	NHDF-Ad	bronchial
10	chr17:46339800-46343200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr17:46339800-46352200	Weak transcription	Primary T cells from cord blood	blood
12	chr17:46341000-46343400	Enhancers	HUVEC	blood vessel
13	chr17:46341400-46343400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr17:46341800-46343200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr17:46341800-46343400	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr17:46341800-46343400	Flanking Active TSS	A549	lung
17	chr17:46341800-46343600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr17:46341800-46343600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr17:46341800-46343800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr17:46341800-46344400	Enhancers	Fetal Intestine Small	intestine
21	chr17:46341800-46344600	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr17:46342000-46343600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr17:46342000-46343800	Enhancers	Osteobl	bone
24	chr17:46342200-46343200	Enhancers	Pancreas	Pancrea
25	chr17:46342200-46343400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr17:46342200-46343600	Enhancers	NHEK	skin
27	chr17:46342200-46343800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr17:46342200-46344800	Enhancers	Fetal Intestine Large	intestine
29	chr17:46342400-46343200	Enhancers	Primary hematopoietic stem cells	blood
30	chr17:46342400-46343400	Enhancers	Duodenum Mucosa	Duodenum
31	chr17:46342400-46343400	Enhancers	NH-A	brain
32	chr17:46342400-46343600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr17:46342400-46343600	Enhancers	Primary T cells fromperipheralblood	blood
34	chr17:46342400-46347800	Weak transcription	Psoas Muscle	Psoas
35	chr17:46342800-46343200	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr17:46342800-46343400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr17:46342800-46343400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr17:46343000-46343200	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr17:46343000-46343400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr17:46343000-46343400	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr17:46343000-46343400	Enhancers	K562	blood
42	chr17:46343000-46343600	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr17:46343000-46343600	Active TSS	Stomach Mucosa	stomach
44	chr17:46343000-46343600	Enhancers	GM12878-XiMat	blood
45	chr17:46343000-46343800	Enhancers	Fetal Kidney	kidney

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