Variant report

Variant	rs12663002
Chromosome Location	chr6:28441634-28441635
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28435580..28437630-chr6:28438872..28441704,3	K562	blood:
2	chr6:28439833..28442457-chr6:28444087..28445885,2	K562	blood:
3	chr6:28422985..28425247-chr6:28440349..28442926,2	K562	blood:
4	chr6:28438384..28441784-chr6:28470491..28474037,3	K562	blood:
5	chr6:28436210..28439439-chr6:28440893..28443830,3	K562	blood:
6	chr6:28441214..28445163-chr6:28446286..28449658,4	K562	blood:
7	chr6:28439477..28442256-chr6:28509445..28511862,2	K562	blood:
8	chr6:28302344..28303875-chr6:28441340..28443590,2	K562	blood:
9	chr6:28440403..28442381-chr6:28583746..28585382,2	K562	blood:
10	chr6:28440523..28445742-chr6:28446027..28449241,8	K562	blood:

No data

No data

No data

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1016070	0.83[EUR][1000 genomes]
rs12661782	0.81[CHD][hapmap]
rs16893947	0.85[CHB][hapmap]
rs16893970	0.85[CHB][hapmap]
rs2021745	0.92[CEU][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.83[EUR][1000 genomes]
rs2071966	0.81[CHD][hapmap]
rs213233	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2531813	0.92[CEU][hapmap];0.84[CHD][hapmap];0.83[EUR][1000 genomes]
rs2531814	0.92[CEU][hapmap];0.84[GIH][hapmap];0.83[EUR][1000 genomes]
rs2859372	0.92[CEU][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.83[EUR][1000 genomes]
rs2859373	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs2859374	0.85[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462666	chr6:28417222-28574415	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv601210	chr6:28417222-28574415	Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12663002	ZNF323	cis	cerebellum	SCAN
rs12663002	ZSCAN23	cis	cerebellum	SCAN
rs12663002	ZKSCAN3	cis	cerebellum	SCAN
rs12663002	ZNF323	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28436800-28442400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:28438600-28442400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:28441600-28442000	Enhancers	K562	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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