Variant report

Variant	rs6049347
Chromosome Location	chr20:24013827-24013828
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs16986162	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3848801	0.85[ASN][1000 genomes]
rs6036614	0.98[EUR][1000 genomes]
rs6036617	0.97[ASN][1000 genomes]
rs6036619	1.00[ASN][1000 genomes]
rs6049337	1.00[ASN][1000 genomes]
rs6049338	1.00[ASN][1000 genomes]
rs6049345	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049348	1.00[ASN][1000 genomes]
rs6049349	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049350	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049351	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114415	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114419	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114422	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6114423	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6114424	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62195285	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7344251	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv833944	chr20:23806288-24021865	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1063474	chr20:23918394-24048069	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1056491	chr20:23955040-24105080	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv585731	chr20:23989027-24024259	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6049347	FAM154B	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24012400-24014000	Enhancers	Primary B cells from peripheral blood	blood
2	chr20:24012400-24014600	Enhancers	Primary T cells from cord blood	blood
3	chr20:24012400-24014600	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr20:24012400-24014600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr20:24012400-24015600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr20:24012600-24014400	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr20:24012600-24014600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr20:24012600-24014600	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr20:24012600-24014800	Enhancers	Primary T cells fromperipheralblood	blood
10	chr20:24013000-24014000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr20:24013000-24014000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr20:24013200-24014000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr20:24013400-24014200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr20:24013400-24014200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
15	chr20:24013600-24014000	Enhancers	Fetal Thymus	thymus
16	chr20:24013800-24014200	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr20:24013800-24014200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
18	chr20:24013800-24014200	Flanking Active TSS	Dnd41	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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