Variant report

Variant	rs2865798
Chromosome Location	chr4:98425582-98425583
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs13135061	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4482769	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879640	chr4:97711707-98697586	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv879641	chr4:98317295-98506794	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv879642	chr4:98317295-98569259	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv879643	chr4:98317295-99065480	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv1835978	chr4:98330337-98469951	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv1833751	chr4:98330337-98471647	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	esv1841838	chr4:98333918-98443617	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv594921	chr4:98333918-98469951	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv879644	chr4:98333918-98506794	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv830016	chr4:98360907-98550751	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv879645	chr4:98371858-98497853	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv879646	chr4:98386631-98569259	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv868914	chr4:98416047-98969285	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	esv2550392	chr4:98424040-98425746	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	n/a
15	esv3335006	chr4:98424329-98426277	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	n/a
16	nsv594932	chr4:98425582-98595080	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2865798	ADH7	cis	cerebellum	SCAN
rs2865798	PPP3CA	cis	cerebellum	SCAN
rs2865798	RAP1GDS1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:98420600-98425600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr4:98421000-98425600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr4:98421000-98426000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr4:98422200-98425600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:98422400-98428600	Weak transcription	HMEC	breast
6	chr4:98425200-98427000	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr4:98425400-98425600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr4:98425400-98426800	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr4:98425400-98426800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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

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