Variant report

Variant	rs270020
Chromosome Location	chr6:128209417-128209418
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1089650	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1089655	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs149805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs156060	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs156065	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs198526	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs198527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs270016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs270017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs270018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs270019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs270021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs436868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs802705	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs802706	0.92[ASN][1000 genomes]
rs802707	0.83[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs802710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs802714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs802754	0.82[EUR][1000 genomes];0.87[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	esv1849854	chr6:128143774-128287313	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv1024516	chr6:128184182-128298278	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs270020	C6orf190	cis	multi-tissue	Pritchard
rs270020	THEMIS	cis	Lymphoblastoid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128196600-128211600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr6:128201000-128214600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:128206200-128212400	Strong transcription	Fetal Thymus	thymus
4	chr6:128207600-128213000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
5	chr6:128208000-128210400	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr6:128208000-128212800	Weak transcription	Thymus	Thymus
7	chr6:128208600-128210000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr6:128208800-128210400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:128209200-128209600	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr6:128209200-128210000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:128209200-128210200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr6:128209200-128210400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr6:128209400-128210200	Weak transcription	Primary T cells from cord blood	blood
14	chr6:128209400-128210200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr6:128209400-128210800	Enhancers	Dnd41	blood
16	chr6:128209400-128212200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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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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