Variant report

Variant	rs10734999
Chromosome Location	chr12:1780565-1780566
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10744548	1.00[CHB][hapmap]
rs10773979	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10848554	1.00[CHB][hapmap]
rs10848568	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap]
rs11836547	1.00[CHB][hapmap]
rs12370189	0.85[CHB][hapmap]
rs4140993	1.00[CHB][hapmap]
rs7134070	1.00[CHB][hapmap]
rs7138701	1.00[CHB][hapmap]
rs7302234	1.00[CHB][hapmap]
rs7311218	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7488369	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs767870	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs7975375	0.91[CEU][hapmap]
rs9805042	1.00[CHB][hapmap];0.94[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv898584	chr12:1607390-1783251	Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10734999	KDM5A	cis	parietal	SCAN
rs10734999	PARP11	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1775200-1781200	Enhancers	Fetal Intestine Small	intestine
2	chr12:1777400-1781000	Enhancers	Fetal Intestine Large	intestine
3	chr12:1777800-1780600	Enhancers	Hela-S3	cervix
4	chr12:1778200-1781000	Enhancers	Stomach Mucosa	stomach
5	chr12:1778400-1780600	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr12:1778800-1780600	Enhancers	HepG2	liver
7	chr12:1779200-1780600	Enhancers	Liver	Liver
8	chr12:1779600-1780800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
9	chr12:1779600-1782200	Weak transcription	Small Intestine	intestine
10	chr12:1779800-1780600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:1780200-1780800	Weak transcription	Colonic Mucosa	Colon
12	chr12:1780200-1780800	Enhancers	Duodenum Mucosa	Duodenum
13	chr12:1780200-1781000	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr12:1780400-1781600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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