Variant report

Variant	rs59939954
Chromosome Location	chr6:117936425-117936426
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10484300	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11153673	0.83[AFR][1000 genomes]
rs11153683	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11153684	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11153694	0.83[AFR][1000 genomes]
rs11752432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11754163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11754321	0.83[AFR][1000 genomes]
rs11754460	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11754754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11755139	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11756843	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11757765	0.83[AFR][1000 genomes]
rs11758182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11758857	0.83[AFR][1000 genomes]
rs11758954	0.83[AFR][1000 genomes]
rs11961026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11961502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11964717	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11965618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11967810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12464	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12665046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12665080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13197163	0.83[AFR][1000 genomes]
rs13197261	0.83[AFR][1000 genomes]
rs13206727	0.83[AFR][1000 genomes]
rs13217247	0.83[AFR][1000 genomes]
rs2301424	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28787987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35230921	0.83[AFR][1000 genomes]
rs35282633	0.83[AFR][1000 genomes]
rs35957877	0.83[AFR][1000 genomes]
rs57261661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs958904	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9766138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9766317	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][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	nsv532050	chr6:117528154-118203005	ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	esv3333863	chr6:117935959-117940757	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:117929400-117938600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:117931600-117937000	Weak transcription	Placenta	Placenta
3	chr6:117931800-117937000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:117933200-117936600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:117934200-117938600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:117934400-117936800	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr6:117934400-117937000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:117934600-117936600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:117934800-117936600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr6:117934800-117936800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:117934800-117937400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:117935200-117936600	Weak transcription	NH-A	brain
13	chr6:117935400-117936600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:117935400-117937000	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr6:117935400-117937000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:117935400-117937000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:117935600-117936600	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr6:117935600-117936800	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr6:117935600-117936800	Weak transcription	Osteobl	bone
20	chr6:117935600-117937200	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr6:117935800-117936600	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr6:117935800-117936800	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr6:117935800-117937200	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr6:117936000-117937200	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr6:117936200-117936800	Enhancers	H1 Cell Line	embryonic stem cell
26	chr6:117936200-117938400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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