Variant report

Variant	rs1839491
Chromosome Location	chr3:161126429-161126430
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:161009100..161011704-chr3:161125007..161126945,2	MCF-7	breast:
2	chr3:161003253..161016100-chr3:161121496..161137189,33	MCF-7	breast:
3	chr3:161124593..161126837-chr3:161161985..161163633,2	MCF-7	breast:
4	chr3:160943414..160948630-chr3:161124537..161130455,7	MCF-7	breast:
5	chr3:160641537..160644034-chr3:161124044..161126884,2	MCF-7	breast:
6	chr3:160938892..160940455-chr3:161125630..161127177,2	MCF-7	breast:
7	chr3:160934874..160951087-chr3:161118055..161142485,77	MCF-7	breast:
8	chr3:160963270..160965103-chr3:161124970..161126764,2	MCF-7	breast:
9	chr3:160819969..160822199-chr3:161125222..161127254,2	MCF-7	breast:
10	chr3:161040460..161042970-chr3:161125296..161126963,2	MCF-7	breast:
11	chr3:161125406..161127626-chr3:161276162..161278825,2	MCF-7	breast:
12	chr3:161033236..161036164-chr3:161124055..161126623,3	MCF-7	breast:
13	chr3:160992477..160993038-chr3:161126344..161127297,2	MCF-7	breast:
14	chr14:24695117..24696996-chr3:161125518..161127057,2	MCF-7	breast:
15	chr17:57919104..57921742-chr3:161124811..161126893,2	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11710086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11710916	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11713185	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1349352	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16832246	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16832279	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1811483	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2061804	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34727114	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs404725	0.90[ASN][1000 genomes]
rs456882	0.83[ASN][1000 genomes]
rs458175	0.82[ASN][1000 genomes]
rs460950	0.83[ASN][1000 genomes]
rs463630	0.83[ASN][1000 genomes]
rs463890	0.82[ASN][1000 genomes]
rs466971	0.82[ASN][1000 genomes]
rs467458	0.83[ASN][1000 genomes]
rs67077657	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73021449	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
3	nsv829772	chr3:161047817-161202554	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv877710	chr3:161087857-161245414	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	84 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1839491	SPTSSB	cis	Thyroid	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161113600-161127600	Weak transcription	NHEK	skin
2	chr3:161121200-161126600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:161121400-161126800	Weak transcription	Hela-S3	cervix
4	chr3:161123000-161127400	Enhancers	HepG2	liver
5	chr3:161123200-161132000	Enhancers	Stomach Mucosa	stomach
6	chr3:161124000-161133400	Weak transcription	Fetal Lung	lung
7	chr3:161124800-161126800	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr3:161124800-161127000	Weak transcription	HMEC	breast
9	chr3:161124800-161131000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr3:161124800-161131000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:161125000-161127000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:161125200-161126600	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr3:161125200-161126800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr3:161125600-161129600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:161125600-161137000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:161126200-161131000	Weak transcription	Gastric	stomach
17	chr3:161126400-161126800	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr3:161126400-161126800	Enhancers	Liver	Liver
19	chr3:161126400-161127600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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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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