Variant report

Variant	rs2124006
Chromosome Location	chr6:73958442-73958443
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	6:73955774-73958859..6:74078047-74099067	Hela-S3	cervix:
2	6:73955774-73958859..6:74099986-74112890	Hela-S3	cervix:
3	6:73955774-73958859..6:74062967-74076046	GM12878	blood:
4	6:73955774-73958859..6:74160392-74184826	Hela-S3	cervix:
5	6:73927031-73938730..6:73955774-73958859	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000207023	Chromatin interaction
ENSG00000231332	Chromatin interaction
ENSG00000135297	Chromatin interaction
ENSG00000235174	Chromatin interaction
ENSG00000203908	Chromatin interaction
ENSG00000164430	Chromatin interaction
ENSG00000238464	Chromatin interaction
ENSG00000256980	Chromatin interaction
ENSG00000203909	Chromatin interaction
ENSG00000080007	Chromatin interaction
ENSG00000203907	Chromatin interaction
ENSG00000224221	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10455092	0.84[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap]
rs12153835	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs12208781	0.89[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs12216162	0.89[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs12529624	0.81[ASN][1000 genomes]
rs12529658	0.81[ASN][1000 genomes]
rs12530079	0.89[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs13212903	0.81[ASN][1000 genomes]
rs13213885	0.81[ASN][1000 genomes]
rs1555443	0.81[ASN][1000 genomes]
rs1869559	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs1891494	1.00[ASW][hapmap];0.83[CHD][hapmap];0.81[LWK][hapmap];0.84[MEX][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1970551	0.81[ASN][1000 genomes]
rs2124004	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs2168113	0.84[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap]
rs2254630	0.81[ASN][1000 genomes]
rs2603471	0.84[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap]
rs2797086	0.86[ASN][1000 genomes]
rs34531450	0.81[ASN][1000 genomes]
rs4706533	0.84[ASN][1000 genomes]
rs4706534	0.84[ASN][1000 genomes]
rs4708041	0.84[ASN][1000 genomes]
rs4708042	0.89[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs502107	0.89[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs502282	0.89[CHB][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs509406	0.81[ASN][1000 genomes]
rs511219	0.84[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs512366	0.82[ASN][1000 genomes]
rs555779	0.84[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap]
rs576229	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs579736	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs61493410	0.82[ASN][1000 genomes]
rs62438232	0.81[ASN][1000 genomes]
rs62438233	0.81[ASN][1000 genomes]
rs62438235	0.81[ASN][1000 genomes]
rs62438239	0.81[ASN][1000 genomes]
rs6453659	1.00[ASW][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6453660	0.82[ASW][hapmap];0.94[MKK][hapmap]
rs6904505	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7382700	0.83[ASN][1000 genomes]
rs7740081	0.84[ASN][1000 genomes]
rs7742847	0.81[ASN][1000 genomes]
rs7743609	0.81[ASN][1000 genomes]
rs7744174	0.84[ASN][1000 genomes]
rs7759315	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs7765618	0.81[ASN][1000 genomes]
rs7769905	0.84[CHB][hapmap]
rs9800824	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1022151	chr6:73876795-73996828	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv538304	chr6:73876795-73996828	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1030079	chr6:73920050-73984084	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv886157	chr6:73922561-73969722	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
6	esv3416786	chr6:73925761-73958538	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
7	esv3381844	chr6:73929080-73961109	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2124006	KHDC1	cis	cerebellum	SCAN
rs2124006	EEF1A1	cis	parietal	SCAN
rs2124006	KHDC1	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:73934000-73972400	Weak transcription	Ovary	ovary
2	chr6:73950400-73972200	Weak transcription	Right Atrium	heart
3	chr6:73957800-73971600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:73958200-73972400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:73958400-73959600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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