Variant report

Variant	rs2123344
Chromosome Location	chr17:46339612-46339613
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46292663..46294856-chr17:46339280..46340993,2	MCF-7	breast:
2	chr17:46297000..46299844-chr17:46338124..46340489,2	K562	blood:
3	chr17:46328583..46331168-chr17:46336391..46339869,3	K562	blood:
4	chr17:46338241..46340530-chr17:46665997..46668166,2	K562	blood:
5	chr17:46338278..46339846-chr17:46409722..46411626,2	K562	blood:
6	chr17:46328637..46331168-chr17:46337351..46339869,2	K562	blood:
7	chr17:46334050..46336909-chr17:46339101..46341476,2	K562	blood:
8	chr17:46338702..46340433-chr17:46342377..46345030,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000120093	Chromatin interaction
ENSG00000233101	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12603827	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12937347	0.88[ASN][1000 genomes]
rs1396868	0.80[ASN][1000 genomes]
rs1509635	0.82[JPT][hapmap]
rs1553750	0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs2924250	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	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2938470	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs4239201	0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4324172	0.90[ASN][1000 genomes]
rs4423463	0.92[ASN][1000 genomes]
rs4606751	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4793816	0.86[ASN][1000 genomes]
rs6504160	0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6504210	0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7211099	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7211780	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs7213149	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7216202	0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7218563	0.92[ASN][1000 genomes]
rs7221510	0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs8072002	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs8077516	0.90[ASN][1000 genomes]
rs8077763	0.88[ASN][1000 genomes]
rs9303541	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs9797269	0.84[ASN][1000 genomes]
rs9898383	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs9906658	0.86[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2123344	CCR10	cis	parietal	SCAN
rs2123344	GOSR2	cis	parietal	SCAN
rs2123344	CDK5RAP3	cis	parietal	SCAN
rs2123344	CDK5RAP3	cis	cerebellum	SCAN

Chromatin state (count:32 , 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	chr17:46322600-46341800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr17:46322600-46342200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr17:46322800-46356200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr17:46323000-46370800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr17:46324200-46355800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr17:46324200-46371600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr17:46324800-46343000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr17:46326200-46361200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr17:46336200-46340200	Weak transcription	Fetal Kidney	kidney
11	chr17:46336200-46342400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr17:46337000-46343000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr17:46337200-46341800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr17:46337200-46341800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr17:46337600-46340200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr17:46337600-46341400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr17:46338000-46342400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr17:46338200-46341400	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr17:46338600-46339800	Strong transcription	Primary T cells from cord blood	blood
20	chr17:46338800-46339800	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr17:46338800-46339800	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr17:46338800-46340800	Weak transcription	Fetal Intestine Small	intestine
23	chr17:46338800-46342200	Weak transcription	Fetal Intestine Large	intestine
24	chr17:46339000-46341000	Enhancers	A549	lung
25	chr17:46339000-46341800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr17:46339000-46343000	Weak transcription	K562	blood
27	chr17:46339200-46343400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr17:46339400-46342800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr17:46339400-46343600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr17:46339600-46341000	Weak transcription	HUVEC	blood vessel
31	chr17:46339600-46343000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr17:46339600-46343800	Enhancers	NHDF-Ad	bronchial

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