Variant report

Variant	rs1233666
Chromosome Location	chr6:28176415-28176416
allele	G/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28175786..28178014-chr6:28179307..28182825,4	MCF-7	breast:
2	chr6:28154956..28156603-chr6:28174738..28177213,2	K562	blood:
3	chr6:28174435..28176569-chr6:28303412..28304973,2	MCF-7	breast:
4	chr6:28109035..28111134-chr6:28175130..28176632,2	K562	blood:
5	chr6:28170099..28172681-chr6:28173612..28177819,3	K562	blood:
6	chr6:28174974..28177419-chr6:28322626..28324224,2	K562	blood:
7	chr6:28175915..28177544-chr6:28181092..28183263,2	K562	blood:
8	chr6:27864015..27866427-chr6:28176005..28180203,3	K562	blood:
9	chr6:28154709..28159711-chr6:28172250..28177968,6	K562	blood:
10	chr6:28174164..28176650-chr6:28369447..28371283,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000218016	Chromatin interaction
ENSG00000238610	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10484404	0.90[CEU][hapmap]
rs1062169	0.94[GIH][hapmap];0.83[TSI][hapmap]
rs1150697	0.81[CEU][hapmap]
rs1150698	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1150699	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1150704	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1150714	0.80[CEU][hapmap]
rs11752073	0.90[CEU][hapmap]
rs11758148	1.00[CEU][hapmap]
rs1233664	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1233665	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1474589	0.80[CEU][hapmap]
rs16893552	0.80[CEU][hapmap]
rs16893817	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs16893937	0.80[CEU][hapmap]
rs16901846	0.80[CEU][hapmap]
rs1736890	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1736894	1.00[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1778469	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1778477	0.91[GIH][hapmap]
rs1890809	0.90[CEU][hapmap]
rs2232422	0.80[CEU][hapmap]
rs2281043	0.80[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap]
rs2622315	0.90[CEU][hapmap]
rs3800325	0.80[CEU][hapmap]
rs4141691	0.80[CEU][hapmap]
rs6456811	0.80[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap]
rs6917759	0.90[CEU][hapmap]
rs6923170	0.80[CEU][hapmap]
rs6929559	0.90[CEU][hapmap]
rs73740584	0.84[EUR][1000 genomes]
rs7744788	0.80[CEU][hapmap]
rs7769054	1.00[CEU][hapmap]
rs993619	1.00[CEU][hapmap];0.81[GIH][hapmap];0.88[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	nsv883514	chr6:28155418-28185726	Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv883515	chr6:28156476-28181675	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv883516	chr6:28156476-28185726	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1233666	ZSCAN23	cis	cerebellum	SCAN
rs1233666	PARD6B	trans	cerebellum	SCAN
rs1233666	ZNF323	cis	parietal	SCAN
rs1233666	ZSCAN23	cis	parietal	SCAN
rs1233666	ZNF165	cis	parietal	SCAN
rs1233666	AL022393.7	cis	Thyroid	GTEx
rs1233666	HFE	cis	cerebellum	SCAN
rs1233666	HIST1H4C	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28174600-28176600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:28174800-28176600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr6:28174800-28176600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:28175800-28176600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:28175800-28177600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:28176200-28176600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
7	chr6:28176400-28176600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
8	chr6:28176400-28176600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
9	chr6:28176400-28176600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
10	chr6:28176400-28176600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
11	chr6:28176400-28177600	Weak transcription	HMEC	breast

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