Variant report

Variant	rs10477538
Chromosome Location	chr5:115070403-115070404
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115069007..115070824-chr5:115175846..115177904,2	K562	blood:
2	chr5:114960202..114961794-chr5:115068533..115071255,2	K562	blood:

Variant related genes	Relation type
ENSG00000251201	Chromatin interaction
ENSG00000134970	Chromatin interaction
ENSG00000177879	Chromatin interaction
ENSG00000145782	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10045982	1.00[ASN][1000 genomes]
rs10045984	0.98[ASN][1000 genomes]
rs10050890	0.98[ASN][1000 genomes]
rs10052595	0.98[ASN][1000 genomes]
rs10064258	0.99[ASN][1000 genomes]
rs10067465	0.98[ASN][1000 genomes]
rs10071727	0.98[ASN][1000 genomes]
rs10071991	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10074993	1.00[ASN][1000 genomes]
rs10075659	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10080052	0.99[ASN][1000 genomes]
rs10440764	1.00[ASN][1000 genomes]
rs10477537	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10478244	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10478245	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10478246	0.98[ASN][1000 genomes]
rs10478247	0.96[ASN][1000 genomes]
rs10478248	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10478249	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10478250	1.00[ASN][1000 genomes]
rs10478252	0.86[ASN][1000 genomes]
rs10478253	1.00[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1121481	0.88[ASN][1000 genomes]
rs11740930	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11742950	1.00[ASN][1000 genomes]
rs11747871	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11748556	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11750906	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12651799	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12654416	0.88[ASN][1000 genomes]
rs12655946	0.98[ASN][1000 genomes]
rs13159452	0.98[ASN][1000 genomes]
rs13164173	0.97[ASN][1000 genomes]
rs13164466	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13186692	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13355215	0.91[ASN][1000 genomes]
rs13356510	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[ASN][1000 genomes]
rs13358666	0.98[ASN][1000 genomes]
rs13360159	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13360899	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13361948	1.00[ASN][1000 genomes]
rs13362015	1.00[ASN][1000 genomes]
rs1363358	1.00[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[ASN][1000 genomes]
rs1363359	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1363360	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1960911	0.98[ASN][1000 genomes]
rs34871962	1.00[ASN][1000 genomes]
rs35290049	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35502695	0.98[ASN][1000 genomes]
rs35518456	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35828343	0.98[ASN][1000 genomes]
rs59934775	0.96[ASN][1000 genomes]
rs67475015	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72800476	0.82[ASN][1000 genomes]
rs9326972	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[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	nsv916273	chr5:114656592-115089901	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv1024641	chr5:115030110-115123474	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1021139	chr5:115036724-115131280	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10477538	TSSK1B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115060600-115081000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:115067000-115070600	Enhancers	Liver	Liver
3	chr5:115068800-115072200	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr5:115069000-115071600	Enhancers	Adipose Nuclei	Adipose
5	chr5:115069200-115072200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr5:115069200-115074400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr5:115069400-115070800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr5:115069400-115071000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr5:115069600-115070600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr5:115069600-115071000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:115069800-115070800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:115069800-115071000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr5:115070000-115071200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr5:115070000-115071600	Enhancers	H9 Cell Line	embryonic stem cell
15	chr5:115070200-115071600	Enhancers	Primary B cells from peripheral blood	blood
16	chr5:115070200-115073400	Enhancers	H1 Cell Line	embryonic stem cell
17	chr5:115070400-115071200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:115070400-115071600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links