Variant report

Variant	rs2142704
Chromosome Location	chr6:27530562-27530563
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27518662..27523972-chr6:27530343..27535715,8	K562	blood:
2	chr6:27529825..27532191-chr6:27536360..27538063,2	K562	blood:
3	chr6:27530455..27532124-chr6:27543501..27545460,2	K562	blood:
4	chr6:27098876..27101009-chr6:27528408..27531042,2	K562	blood:

Variant related genes	Relation type
ENSG00000124635	Chromatin interaction
ENSG00000196787	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1028311	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10946943	0.89[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap]
rs1157432	0.89[CEU][hapmap];0.80[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs12055685	0.87[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap]
rs16867916	0.88[CEU][hapmap];0.93[JPT][hapmap]
rs16867976	0.87[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs2142706	0.89[CEU][hapmap]
rs2143062	0.83[MKK][hapmap]
rs2143082	0.81[EUR][1000 genomes]
rs2205828	0.82[ASN][1000 genomes]
rs4236044	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4711157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4713114	0.84[EUR][1000 genomes]
rs6456790	1.00[YRI][hapmap]
rs6456798	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6906653	0.88[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap]
rs6908024	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6911283	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6920044	0.89[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap]
rs6934295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73739763	0.90[EUR][1000 genomes]
rs7763685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9357044	0.89[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap]
rs9368524	0.89[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap]
rs9379994	0.83[EUR][1000 genomes]
rs9379995	0.92[EUR][1000 genomes]
rs9380001	0.89[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs9393826	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9393832	1.00[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes]
rs9393835	0.90[EUR][1000 genomes]
rs9393836	0.90[EUR][1000 genomes]
rs9393838	0.90[EUR][1000 genomes]
rs9393839	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9461389	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9461392	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9468157	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468158	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs970668	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]

Variant overlapped rSNPs/rCNVs (count:12 , 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
10	nsv883509	chr6:27492906-27586181	Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv1018107	chr6:27503525-27596736	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv538168	chr6:27503525-27596736	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2142704	HIST1H2BJ	cis	cerebellum	SCAN
rs2142704	HIST1H3C	cis	parietal	SCAN
rs2142704	HIST1H2BE	cis	cerebellum	SCAN
rs2142704	ZNF391	cis	cerebellum	SCAN
rs2142704	ZSCAN23	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27526600-27533400	Weak transcription	GM12878-XiMat	blood
2	chr6:27530000-27530600	Active TSS	K562	blood
3	chr6:27530000-27531800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:27530000-27533200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr6:27530000-27533200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:27530200-27531000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:27530200-27531200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:27530200-27533400	Weak transcription	HMEC	breast
9	chr6:27530400-27533200	Weak transcription	A549	lung

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