Variant report

Variant	rs10007887
Chromosome Location	chr4:10749071-10749072
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10002150	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10516209	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10516211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10805246	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10805247	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10938948	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11938512	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11946994	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12643478	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12644098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12648342	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16872866	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16872935	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28532032	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28729671	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4073342	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4368597	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4420973	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4441748	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4470616	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4485814	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4629442	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6817400	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6828448	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6831297	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6846210	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6848219	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73105702	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7658643	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7676338	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7681266	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7683803	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9291448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9291449	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9884398	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530280	chr4:9947818-10940041	Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases
2	nsv869057	chr4:10013411-10875454	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
3	nsv997936	chr4:10040713-11009045	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
4	nsv517971	chr4:10399068-10893253	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv878694	chr4:10407572-10783606	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv878697	chr4:10501373-10831866	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv829860	chr4:10598743-10764854	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv822488	chr4:10709164-10784711	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1004951	chr4:10723763-10771088	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1000613	chr4:10723763-11716982	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
11	nsv1004121	chr4:10738618-11057063	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv878699	chr4:10744931-10874933	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv532707	chr4:10747826-11705504	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10007887	HS3ST1	Cis_1M	lymphoblastoid	RTeQTL
rs10007887	MRFAP1L1	cis	parietal	SCAN
rs10007887	TBC1D14	cis	parietal	SCAN
rs10007887	AFAP1	cis	parietal	SCAN
rs10007887	HS3ST1	cis	lymphoblastoid	seeQTL
rs10007887	PPP2R2C	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:10743600-10752600	Weak transcription	Osteobl	bone
2	chr4:10746800-10749600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr4:10746800-10749600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr4:10747600-10749200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr4:10747800-10749200	Enhancers	HSMM	muscle
6	chr4:10747800-10749600	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr4:10748000-10749200	Enhancers	Colon Smooth Muscle	Colon
8	chr4:10748200-10749200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:10748400-10750600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr4:10748600-10749200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:10748600-10749200	Enhancers	Primary B cells from peripheral blood	blood
12	chr4:10748600-10749200	Enhancers	Ovary	ovary
13	chr4:10748800-10749200	Active TSS	GM12878-XiMat	blood
14	chr4:10748800-10749800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:10749000-10749200	Enhancers	Primary B cells from cord blood	blood
16	chr4:10749000-10749200	Enhancers	HSMMtube	muscle
17	chr4:10749000-10752000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:10749000-10755200	Weak transcription	Fetal Muscle Leg	muscle

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