Variant report

Variant	rs10056974
Chromosome Location	chr5:61564052-61564053
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:61550007..61554674-chr5:61558868..61565665,10	K562	blood:
2	chr5:61560375..61564102-chr5:61592918..61596892,3	K562	blood:
3	chr5:61561722..61564557-chr5:61699479..61701538,2	K562	blood:
4	chr5:61557476..61560441-chr5:61562160..61565169,3	MCF-7	breast:
5	chr5:61561783..61565148-chr5:61601604..61603284,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000086189	Chromatin interaction
ENSG00000068796	Chromatin interaction
ENSG00000086200	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10038739	0.85[ASN][1000 genomes]
rs10051806	0.85[ASN][1000 genomes]
rs10052005	0.85[ASN][1000 genomes]
rs10061970	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10471273	0.85[ASN][1000 genomes]
rs10471539	0.85[ASN][1000 genomes]
rs10471541	0.85[ASN][1000 genomes]
rs1108159	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.90[LWK][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12332195	0.85[ASN][1000 genomes]
rs13358776	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16890608	1.00[CEU][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17366217	0.85[ASN][1000 genomes]
rs17381617	0.84[EUR][1000 genomes]
rs28718571	0.85[ASN][1000 genomes]
rs3776613	0.88[EUR][1000 genomes]
rs3909434	0.85[ASN][1000 genomes]
rs4079571	0.85[ASN][1000 genomes]
rs55721963	0.84[EUR][1000 genomes]
rs55822651	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55951418	0.81[EUR][1000 genomes]
rs57340432	0.85[ASN][1000 genomes]
rs57935172	0.85[ASN][1000 genomes]
rs58431207	0.85[ASN][1000 genomes]
rs58762563	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61008243	0.85[ASN][1000 genomes]
rs61388866	0.86[EUR][1000 genomes]
rs73760588	0.88[EUR][1000 genomes]
rs73760590	0.88[EUR][1000 genomes]
rs7706828	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024090	chr5:61258759-61921150	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2757996	chr5:61403138-61687817	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2759345	chr5:61403138-61748912	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv830318	chr5:61415713-61623320	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1020255	chr5:61451792-62031365	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1027539	chr5:61457762-62000008	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	esv2755585	chr5:61535831-61618595	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	nsv881726	chr5:61556730-61676911	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10056974	UMODL1	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61558400-61564200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr5:61560800-61564400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr5:61561600-61564400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr5:61563200-61564800	Enhancers	Fetal Intestine Small	intestine
5	chr5:61563200-61564800	Enhancers	Hela-S3	cervix
6	chr5:61563200-61565000	Enhancers	Fetal Intestine Large	intestine
7	chr5:61563200-61565000	Enhancers	HMEC	breast
8	chr5:61563400-61565000	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr5:61563400-61565200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr5:61563400-61566600	Weak transcription	K562	blood
11	chr5:61563600-61564400	Enhancers	Small Intestine	intestine
12	chr5:61563600-61564800	Enhancers	NHEK	skin
13	chr5:61564000-61565000	Enhancers	Fetal Kidney	kidney
14	chr5:61564000-61565200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr5:61564000-61565200	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr5:61564000-61565200	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links