Variant report

Variant	rs9308678
Chromosome Location	chr2:113451761-113451762
allele	C/G
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:113345427..113348355-chr2:113448517..113451814,3	MCF-7	breast:
2	chr2:113444971..113447243-chr2:113449701..113451945,3	K562	blood:
3	chr2:113401698..113404474-chr2:113451513..113454636,3	MCF-7	breast:
4	chr2:113450415..113452081-chr2:113453116..113455723,2	MCF-7	breast:
5	chr2:113448771..113451782-chr2:113462370..113466299,3	K562	blood:
6	chr2:113446769..113452405-chr2:113453017..113461667,12	K562	blood:
7	chr2:113343775..113346140-chr2:113450696..113453641,2	K562	blood:
8	chr2:113450142..113452191-chr2:113453793..113456655,2	K562	blood:
9	chr2:113440402..113444876-chr2:113446106..113453600,11	K562	blood:
10	chr2:113397350..113406961-chr2:113434420..113455729,52	K562	blood:
11	chr2:113444435..113446825-chr2:113447700..113452009,3	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10432586	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10432600	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11685224	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11692234	0.82[ASN][1000 genomes]
rs4337479	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4848290	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6746908	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9308677	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1010106	chr2:113394981-113556071	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv526301	chr2:113451498-113495785	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9308678	SLC20A1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113448200-113452200	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr2:113449200-113456800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:113449600-113452200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:113450200-113452000	Enhancers	Spleen	Spleen
5	chr2:113450800-113451800	Enhancers	Dnd41	blood
6	chr2:113450800-113456000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:113450800-113456200	Weak transcription	Primary B cells from cord blood	blood
8	chr2:113451000-113455000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr2:113451000-113455000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:113451200-113456400	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr2:113451400-113454800	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr2:113451400-113455000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:113451400-113455400	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr2:113451600-113452200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr2:113451600-113454400	Weak transcription	K562	blood
16	chr2:113451600-113455400	Weak transcription	GM12878-XiMat	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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