Variant report

Variant	rs4971085
Chromosome Location	chr1:155138222-155138223
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:155053391..155061594-chr1:155138130..155142281,13	MCF-7	breast:
2	chr1:155056491..155066482-chr1:155136760..155147519,21	K562	blood:
3	chr1:155061833..155068204-chr1:155135824..155142287,19	MCF-7	breast:
4	chr1:155095314..155110392-chr1:155134312..155151496,72	MCF-7	breast:
5	chr1:155138080..155140113-chr1:155163279..155166222,2	K562	blood:
6	chr1:155106324..155115462-chr1:155131611..155142074,22	MCF-7	breast:
7	chr1:155094769..155105017-chr1:155135344..155151845,46	MCF-7	breast:
8	chr1:155110931..155113245-chr1:155137097..155138649,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143590	Chromatin interaction
ENSG00000179085	Chromatin interaction
ENSG00000169241	Chromatin interaction
ENSG00000271748	Chromatin interaction
ENSG00000169242	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10157801	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs10908458	1.00[CHB][hapmap]
rs11264337	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264338	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264339	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11799962	0.82[ASN][1000 genomes]
rs12025371	1.00[CHB][hapmap]
rs12028043	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs12127609	0.82[ASN][1000 genomes]
rs12411216	0.83[ASN][1000 genomes]
rs12752585	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904	1.00[CHB][hapmap]
rs2066981	0.83[CHB][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap]
rs2075570	0.82[ASN][1000 genomes]
rs2075571	0.82[JPT][hapmap]
rs28445596	0.81[ASN][1000 genomes]
rs2974935	0.83[ASN][1000 genomes]
rs2974937	0.83[ASN][1000 genomes]
rs2990220	0.80[ASN][1000 genomes]
rs3814316	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs4072037	0.92[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap]
rs4246529	1.00[CHB][hapmap]
rs4276913	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs4276914	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4421576	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4460629	1.00[CHB][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4745	1.00[CHB][hapmap]
rs4971052	0.91[CHB][hapmap]
rs4971059	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs4971066	0.86[CHB][hapmap]
rs4971073	0.86[CHB][hapmap]
rs4971076	0.93[CHB][hapmap];0.82[ASN][1000 genomes]
rs4971079	1.00[CHB][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4971088	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4971089	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4971093	0.80[ASN][1000 genomes]
rs4971100	0.82[JPT][hapmap]
rs6676150	0.93[AFR][1000 genomes]
rs7364524	0.93[CHB][hapmap];0.82[ASN][1000 genomes]
rs7556304	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs760077	0.80[ASN][1000 genomes]
rs914615	0.84[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap]
rs9297	1.00[CHB][hapmap]
rs9426886	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
3	nsv464084	chr1:155082298-155194980	Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
4	nsv547961	chr1:155082298-155194980	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
5	nsv831614	chr1:155094978-155275031	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	434 gene(s)	inside rSNPs	diseases
6	esv2757756	chr1:155094978-155314807	Bivalent Enhancer Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
7	esv2758971	chr1:155094978-155314807	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
8	nsv470741	chr1:155115260-155230131	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	381 gene(s)	inside rSNPs	diseases
9	nsv1010146	chr1:155119096-155201064	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
10	nsv872457	chr1:155135335-155310443	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4971085	GBAP1	cis	lung	GTEx
rs4971085	RP11-263K19.4	cis	Whole Blood	GTEx
rs4971085	THBS3	cis	Whole Blood	GTEx
rs4971085	GBA	cis	Esophagus Mucosa	GTEx
rs4971085	GBAP1	cis	Thyroid	GTEx
rs4971085	GBAP1	cis	Artery Tibial	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155134200-155145000	Weak transcription	Small Intestine	intestine
2	chr1:155137800-155138400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:155138000-155138800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:155138000-155139400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:155138200-155138400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
6	chr1:155138200-155138400	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr1:155138200-155138400	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr1:155138200-155138400	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr1:155138200-155138400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr1:155138200-155138600	Enhancers	H9 Cell Line	embryonic stem cell
11	chr1:155138200-155138600	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr1:155138200-155138600	Enhancers	Adipose Nuclei	Adipose
13	chr1:155138200-155138800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr1:155138200-155138800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
15	chr1:155138200-155139400	Enhancers	Brain Anterior Caudate	brain
16	chr1:155138200-155139600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
17	chr1:155138200-155139600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr1:155138200-155140400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:155138200-155140400	Enhancers	Primary hematopoietic stem cells	blood
20	chr1:155138200-155140600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:155138200-155140600	Enhancers	Fetal Muscle Leg	muscle
22	chr1:155138200-155140600	Enhancers	HUVEC	blood vessel

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