Variant report

Variant	rs6580817
Chromosome Location	chr12:51626196-51626197
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10735832	0.95[JPT][hapmap]
rs10783422	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783423	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876154	0.87[EUR][1000 genomes]
rs10876155	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169761	0.95[JPT][hapmap]
rs1130598	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3888223	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6421171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6580809	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs6580816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7305016	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7307217	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7309376	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7310947	0.90[ASN][1000 genomes]
rs7314235	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7398443	0.85[EUR][1000 genomes]
rs7959901	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51613000-51631800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:51613400-51631600	Weak transcription	Thymus	Thymus
3	chr12:51613400-51631800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr12:51613400-51631800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:51613400-51632000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:51613600-51631800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:51613600-51631800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr12:51613600-51631800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr12:51614200-51631600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr12:51616400-51631600	Weak transcription	Gastric	stomach
11	chr12:51616800-51631800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr12:51619400-51631800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr12:51619600-51631800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr12:51620000-51631800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:51621200-51632000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:51623800-51631600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:51624000-51631800	Weak transcription	Brain Germinal Matrix	brain
18	chr12:51624200-51631600	Weak transcription	Fetal Brain Male	brain

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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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