Variant report

Variant	rs6834470
Chromosome Location	chr4:88148812-88148813
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12649293	0.95[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap]
rs7683063	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698284	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs7698923	0.95[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	25 gene(s)	inside rSNPs	diseases
2	nsv1007020	chr4:88046263-88235018	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537169	chr4:88046263-88235018	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv3336183	chr4:88147028-88149176	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv3370676	chr4:88147378-88148876	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6834470	TIGD2	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88142400-88149800	Weak transcription	K562	blood
2	chr4:88142400-88155200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:88142400-88156400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:88142600-88149400	Weak transcription	HepG2	liver
5	chr4:88145800-88156800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:88148200-88149000	Enhancers	Colonic Mucosa	Colon
7	chr4:88148200-88152000	Enhancers	Fetal Intestine Large	intestine
8	chr4:88148200-88152400	Enhancers	Fetal Intestine Small	intestine
9	chr4:88148400-88149000	Enhancers	Rectal Mucosa Donor 29	rectum
10	chr4:88148400-88149400	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr4:88148400-88149800	Enhancers	Hela-S3	cervix
12	chr4:88148400-88150800	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr4:88148600-88149400	Enhancers	Psoas Muscle	Psoas
14	chr4:88148600-88150000	Enhancers	Stomach Mucosa	stomach
15	chr4:88148600-88150400	Enhancers	Liver	Liver
16	chr4:88148600-88150800	Enhancers	Duodenum Mucosa	Duodenum
17	chr4:88148800-88149400	Enhancers	Skeletal Muscle Female	skeletal muscle

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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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