Variant report

Variant	rs10773979
Chromosome Location	chr12:1788864-1788865
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:1786995..1789598-chr12:1798189..1801520,4	MCF-7	breast:
2	chr12:1783814..1786407-chr12:1787390..1790840,3	MCF-7	breast:
3	chr12:1782061..1785967-chr12:1788388..1791261,4	K562	blood:
4	chr12:1787163..1788876-chr12:1797310..1800151,2	MCF-7	breast:
5	chr12:1770836..1772849-chr12:1788601..1790387,2	K562	blood:

Variant related genes	Relation type
ENSG00000006831	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1058322	0.81[ASN][1000 genomes]
rs10734999	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10735000	0.87[ASN][1000 genomes]
rs10744548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744549	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10744550	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10773981	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10773987	0.87[ASN][1000 genomes]
rs10848554	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10848568	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11832522	1.00[ASN][1000 genomes]
rs11836547	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs12370189	0.85[CHB][hapmap]
rs4140993	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4766414	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs57216374	0.96[ASN][1000 genomes]
rs60523400	0.96[ASN][1000 genomes]
rs703176	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7134070	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7138701	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7302234	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs73040720	0.96[ASN][1000 genomes]
rs7311218	1.00[CHB][hapmap]
rs7488369	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs767870	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7963224	0.96[ASN][1000 genomes]
rs7975375	0.84[CEU][hapmap];0.96[ASN][1000 genomes]
rs9805042	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9805109	0.94[ASN][1000 genomes]
rs9888418	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042863	chr12:1163817-1902302	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv541345	chr12:1163817-1902302	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv832304	chr12:1710249-1868642	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv832305	chr12:1769852-1936054	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10773979	KDM5A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1788000-1789800	Weak transcription	HepG2	liver

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