Variant report

Variant	rs321596
Chromosome Location	chr17:33885736-33885737
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:33883508..33885797-chr17:33888017..33890924,2	MCF-7	breast:
2	chr17:33877720..33881405-chr17:33884956..33887272,3	K562	blood:

Variant related genes	Relation type
ENSG00000267625	Chromatin interaction
ENSG00000267359	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs161182	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs161183	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs161184	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1634684	0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs167691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs178649	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2124246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124247	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs225255	0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.81[ASN][1000 genomes]
rs225282	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs225284	0.85[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225290	0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225293	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225297	0.85[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225299	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225302	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs226088	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs226426	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs226428	0.81[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs226434	0.82[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap]
rs226439	0.82[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap]
rs226441	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs321599	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs321601	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs321607	0.81[CEU][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs321608	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs321616	1.00[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs321617	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs321618	0.85[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs720774	0.83[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7406966	0.81[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
2	nsv908079	chr17:33849869-34034851	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv1060890	chr17:33884124-34011034	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv543318	chr17:33884124-34011034	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs321596	CRLF3	cis	cerebellum	SCAN
rs321596	TBC1D29	cis	cerebellum	SCAN
rs321596	TBC1D29	cis	parietal	SCAN
rs321596	PEX12	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33870400-33888600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr17:33883200-33886000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr17:33883200-33886400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr17:33883400-33888600	Enhancers	Primary hematopoietic stem cells	blood
5	chr17:33883800-33886400	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr17:33885200-33886400	Enhancers	K562	blood

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