Variant report

Variant	rs802707
Chromosome Location	chr6:128232934-128232935
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1089650	0.96[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1089655	0.88[ASN][1000 genomes]
rs149805	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs156060	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs156065	0.88[CHB][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs198526	0.90[ASN][1000 genomes]
rs198527	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs270016	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[ASN][1000 genomes]
rs270017	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs270018	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs270019	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[ASN][1000 genomes]
rs270020	0.83[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs270021	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs436868	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs802705	0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[ASN][1000 genomes]
rs802706	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs802710	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs802714	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs802754	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
3	esv3394071	chr6:128232019-128233225	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers	n/a	n/a	inside rSNPs	diseases
4	esv3473313	chr6:128232066-128233200	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	inside rSNPs	diseases
5	esv3473314	chr6:128232095-128233210	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
6	esv3473315	chr6:128232134-128233123	Weak transcription Enhancers ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs802707	C6orf190	cis	multi-tissue	Pritchard
rs802707	THEMIS	cis	Lymphoblastoid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128224000-128235600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr6:128230000-128233000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr6:128230000-128235600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr6:128231000-128233600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:128231400-128233200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:128232200-128233000	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr6:128232800-128233200	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
8	chr6:128232800-128233200	ZNF genes & repeats	Fetal Thymus	thymus
9	chr6:128232800-128233400	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr6:128232800-128233400	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
11	chr6:128232800-128233800	Strong transcription	Primary T cells fromperipheralblood	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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