Variant report

Variant	rs10877300
Chromosome Location	chr12:59893825-59893826
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10467132	0.99[ASN][1000 genomes]
rs10783971	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10783972	0.97[ASN][1000 genomes]
rs10783973	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783978	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10877283	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877284	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877285	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11173047	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11173048	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11522890	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11610321	0.96[ASN][1000 genomes]
rs12422722	0.97[ASN][1000 genomes]
rs1606708	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1813056	0.98[ASN][1000 genomes]
rs4417319	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4575313	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4760153	0.96[ASN][1000 genomes]
rs7132307	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7135598	0.99[ASN][1000 genomes]
rs7301421	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7304708	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7306830	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7315745	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7957054	0.99[ASN][1000 genomes]
rs7959840	0.96[ASN][1000 genomes]
rs7970398	0.96[ASN][1000 genomes]
rs7979573	0.85[AMR][1000 genomes];1.00[ASN][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	esv2762982	chr12:59659871-60000135	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1042271	chr12:59668468-59993468	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1038467	chr12:59680717-59999008	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv541507	chr12:59680717-59999008	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1049084	chr12:59700333-59993468	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv869425	chr12:59746898-60479741	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv826392	chr12:59805637-59895803	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv899129	chr12:59820966-59941423	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv469413	chr12:59856161-59916767	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10877300	HOXC6	cis	parietal	SCAN
rs10877300	OR6C1	cis	cerebellum	SCAN
rs10877300	DDIT3	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59891800-59894400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:59893400-59894200	Enhancers	H1 Cell Line	embryonic stem cell
3	chr12:59893400-59894600	Enhancers	Brain Hippocampus Middle	brain
4	chr12:59893400-59894800	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr12:59893400-59895000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:59893400-59895000	Enhancers	Primary B cells from peripheral blood	blood
7	chr12:59893400-59895000	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr12:59893400-59895200	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr12:59893400-59895400	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr12:59893400-59895600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr12:59893400-59895800	Enhancers	Primary B cells from cord blood	blood
12	chr12:59893600-59894600	Enhancers	Brain Cingulate Gyrus	brain
13	chr12:59893600-59895400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr12:59893600-59895600	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr12:59893600-59895800	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr12:59893800-59894400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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