Variant report

Variant	rs16953235
Chromosome Location	chr17:46244948-46244949
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46243746..46245329-chr17:46246193..46248900,2	K562	blood:
2	chr17:46244120..46246169-chr17:46266999..46269436,2	K562	blood:
3	chr17:46242593..46245429-chr17:46673241..46675379,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108511	Chromatin interaction
ENSG00000233101	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10514938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11650615	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1472966	1.00[ASW][hapmap];0.88[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];1.00[AFR][1000 genomes]
rs16952265	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16953382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16953461	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16953925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16954078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16954204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16955073	1.00[ASW][hapmap]
rs17695373	1.00[ASW][hapmap];0.88[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];1.00[AFR][1000 genomes]
rs17696392	1.00[ASW][hapmap];0.88[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];1.00[AFR][1000 genomes]
rs41280120	1.00[ASN][1000 genomes]
rs41336845	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7216504	1.00[ASN][1000 genomes]
rs72823527	1.00[ASN][1000 genomes]
rs72823530	1.00[ASN][1000 genomes]
rs72823534	1.00[ASN][1000 genomes]
rs72823591	1.00[ASN][1000 genomes]
rs72823599	1.00[ASN][1000 genomes]
rs72823601	1.00[ASN][1000 genomes]
rs72825504	1.00[ASN][1000 genomes]
rs72825512	1.00[ASN][1000 genomes]
rs72825517	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825548	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825584	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72827814	1.00[AFR][1000 genomes]
rs72827830	1.00[AFR][1000 genomes]
rs72827832	1.00[AFR][1000 genomes]
rs72827834	1.00[AFR][1000 genomes]
rs72827839	1.00[AFR][1000 genomes]
rs8067005	1.00[ASN][1000 genomes]
rs8073371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];1.00[ASN][1000 genomes]
rs9904637	1.00[CHB][hapmap]

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	nsv908576	chr17:46147807-46260366	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs16953235	NPEPPS	cis	cerebellum	SCAN
rs16953235	CDK5RAP3	cis	parietal	SCAN
rs16953235	TTC25	cis	parietal	SCAN
rs16953235	AOC3	cis	parietal	SCAN
rs16953235	KRT17	cis	cerebellum	SCAN
rs16953235	CDK5RAP3	cis	cerebellum	SCAN
rs16953235	SNX11	cis	cerebellum	SCAN
rs16953235	TUBG1	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46216400-46251400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr17:46220800-46249000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr17:46230600-46245000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr17:46236000-46250200	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr17:46238200-46250800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr17:46238600-46246600	Weak transcription	Thymus	Thymus
7	chr17:46239200-46246400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr17:46239200-46253800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr17:46240000-46246600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr17:46240000-46250400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr17:46240200-46246400	Weak transcription	Fetal Thymus	thymus
12	chr17:46240200-46246800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr17:46241000-46245000	Enhancers	GM12878-XiMat	blood
14	chr17:46241000-46250200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr17:46241000-46253200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr17:46241200-46246000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr17:46241200-46247400	Weak transcription	Stomach Mucosa	stomach
18	chr17:46242600-46245200	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr17:46244000-46245000	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr17:46244200-46245000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr17:46244200-46245800	Weak transcription	Primary T cells from cord blood	blood
22	chr17:46244600-46245400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr17:46244600-46245400	Enhancers	Liver	Liver
24	chr17:46244800-46245000	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr17:46244800-46245200	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr17:46244800-46245600	Enhancers	Fetal Intestine Small	intestine
27	chr17:46244800-46249200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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