Variant report

Variant	rs970668
Chromosome Location	chr6:27488602-27488603
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27487122..27488910-chr6:27496646..27499202,2	K562	blood:
2	chr6:27486617..27489499-chr6:27758856..27760750,2	K562	blood:
3	chr6:27486831..27488916-chr6:27500916..27502930,2	MCF-7	breast:
4	chr6:27472071..27474860-chr6:27486354..27488722,3	K562	blood:
5	chr6:27440572..27442573-chr6:27486884..27489686,3	K562	blood:
6	chr6:27485668..27488646-chr6:27758590..27761132,3	K562	blood:
7	chr6:27470088..27471608-chr6:27487269..27490005,2	K562	blood:
8	chr6:27484573..27488622-chr6:27496646..27500202,4	K562	blood:
9	chr6:27469947..27474974-chr6:27485508..27488698,9	K562	blood:

No data

Variant related genes	Relation type
ENSG00000096654	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1028311	0.89[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10946943	0.89[CEU][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs12055685	0.86[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs16867916	0.88[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs2142704	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs2142706	0.89[CEU][hapmap]
rs35142924	0.86[ASN][1000 genomes]
rs4236044	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4711157	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes]
rs6456798	0.83[EUR][1000 genomes]
rs6906653	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs6908024	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6911283	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6920044	0.89[CEU][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs6934295	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7763685	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9357044	0.89[CEU][hapmap];0.82[JPT][hapmap]
rs9368524	0.81[ASW][hapmap];0.89[CEU][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs9380001	0.81[ASW][hapmap];0.89[CEU][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap]
rs9393826	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9393832	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs9461389	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9461392	0.83[EUR][1000 genomes]
rs9468157	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs9468158	0.95[AFR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830617	chr6:27424769-27598595	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv462665	chr6:27458013-27547792	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv601203	chr6:27458013-27547792	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1030256	chr6:27477726-27605842	Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv1025862	chr6:27480227-27605321	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv1017347	chr6:27483816-27605842	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv1025572	chr6:27487852-27604454	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv538167	chr6:27487852-27604454	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs970668	HIST1H3C	cis	parietal	SCAN
rs970668	ZSCAN23	cis	cerebellum	SCAN
rs970668	ZNF391	cis	cerebellum	SCAN
rs970668	HIST1H2BJ	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27487600-27490600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr6:27488000-27491600	Weak transcription	K562	blood

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