Variant report

Variant	rs3989103
Chromosome Location	chr8:11306846-11306847
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr8:11306535-11306912	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr8:11306168-11306994	U87	brain:	n/a	n/a
3	POLR2A	chr8:11305791-11307062	U87	brain:	n/a	n/a
4	POLR2A	chr8:11305928-11307021	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:11306300..11308613-chr8:11308996..11313515,5	K562	blood:
2	chr8:11306364..11309144-chr8:11311400..11314118,3	MCF-7	breast:

Variant related genes	Relation type
FAM167A	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10088323	0.82[ASN][1000 genomes]
rs10448145	0.84[ASN][1000 genomes]
rs10448146	0.81[ASN][1000 genomes]
rs10903338	0.81[ASN][1000 genomes]
rs11250136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11250137	0.94[ASN][1000 genomes]
rs11777505	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11779875	0.88[ASN][1000 genomes]
rs11782375	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11785710	0.82[ASN][1000 genomes]
rs11991448	0.89[ASN][1000 genomes]
rs11991453	0.96[ASN][1000 genomes]
rs12543308	0.95[ASN][1000 genomes]
rs12549796	0.81[ASN][1000 genomes]
rs13248746	0.94[ASN][1000 genomes]
rs13264212	0.89[ASN][1000 genomes]
rs2003422	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2003423	0.87[ASN][1000 genomes]
rs2409767	0.91[ASN][1000 genomes]
rs2409770	0.90[ASN][1000 genomes]
rs2409771	0.91[ASN][1000 genomes]
rs2409772	0.98[ASN][1000 genomes]
rs2409773	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2409774	0.98[ASN][1000 genomes]
rs2409775	0.98[ASN][1000 genomes]
rs34013904	0.81[ASN][1000 genomes]
rs35161715	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35433745	0.87[ASN][1000 genomes]
rs4581006	0.92[ASN][1000 genomes]
rs4840560	0.98[ASN][1000 genomes]
rs4840561	0.86[ASN][1000 genomes]
rs4840562	0.81[ASN][1000 genomes]
rs4841533	0.97[ASN][1000 genomes]
rs4841534	0.98[ASN][1000 genomes]
rs4841535	0.97[ASN][1000 genomes]
rs4841536	0.98[ASN][1000 genomes]
rs4841537	0.98[ASN][1000 genomes]
rs4841539	0.97[ASN][1000 genomes]
rs4841540	0.83[ASN][1000 genomes]
rs4841542	0.82[ASN][1000 genomes]
rs58004460	0.89[ASN][1000 genomes]
rs6601589	0.94[ASN][1000 genomes]
rs6983820	0.97[ASN][1000 genomes]
rs6998387	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7830445	0.89[ASN][1000 genomes]
rs9693089	0.81[ASN][1000 genomes]
rs9792166	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9792175	0.98[ASN][1000 genomes]
rs9792227	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9792375	0.89[ASN][1000 genomes]
rs9792397	0.88[ASN][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	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1022525	chr8:11066191-11309356	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv539474	chr8:11066191-11309356	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	esv34097	chr8:11177372-11489894	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv470183	chr8:11236975-11307118	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv465465	chr8:11245064-11307118	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS 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	8 gene(s)	inside rSNPs	diseases
9	nsv610275	chr8:11245064-11307118	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv522860	chr8:11253879-11330364	Bivalent/Poised TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv890357	chr8:11286146-11330364	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1030756	chr8:11292073-11332782	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv1022074	chr8:11292256-11394526	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3989103	C8orf13	Cis_1M	lymphoblastoid	RTeQTL
rs3989103	BLK	Cis_1M	lymphoblastoid	RTeQTL
rs3989103	FAM167A	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11280600-11308800	Weak transcription	Primary B cells from cord blood	blood
2	chr8:11287800-11313600	Weak transcription	Right Atrium	heart
3	chr8:11292400-11313000	Weak transcription	Pancreas	Pancrea
4	chr8:11296200-11319200	Enhancers	Fetal Thymus	thymus
5	chr8:11298800-11308600	Weak transcription	Primary B cells from peripheral blood	blood
6	chr8:11303600-11323200	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr8:11304600-11308200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr8:11304600-11308400	Weak transcription	Thymus	Thymus
9	chr8:11305000-11307400	Enhancers	Brain Anterior Caudate	brain
10	chr8:11305200-11307800	Enhancers	Placenta	Placenta
11	chr8:11305800-11307000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr8:11305800-11307600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr8:11305800-11308200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr8:11305800-11308200	Enhancers	Fetal Brain Female	brain
15	chr8:11305800-11308200	Enhancers	Osteobl	bone
16	chr8:11305800-11310600	Enhancers	Brain Substantia Nigra	brain
17	chr8:11305800-11312200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr8:11306000-11307000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr8:11306000-11307000	Enhancers	HSMM	muscle
20	chr8:11306000-11307200	Enhancers	Muscle Satellite Cultured Cells	--
21	chr8:11306000-11307200	Enhancers	Fetal Heart	heart
22	chr8:11306000-11307200	Enhancers	Left Ventricle	heart
23	chr8:11306000-11307200	Enhancers	HSMMtube	muscle
24	chr8:11306000-11307400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr8:11306000-11307800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr8:11306000-11308000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr8:11306000-11308600	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr8:11306000-11310400	Enhancers	Brain Angular Gyrus	brain
29	chr8:11306000-11310400	Enhancers	Brain Cingulate Gyrus	brain
30	chr8:11306000-11310400	Enhancers	Brain Hippocampus Middle	brain
31	chr8:11306200-11307000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr8:11306200-11307400	Weak transcription	Fetal Kidney	kidney
33	chr8:11306200-11307800	Enhancers	Fetal Brain Male	brain
34	chr8:11306400-11307000	Enhancers	Right Ventricle	heart
35	chr8:11306400-11307400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr8:11306400-11311800	Weak transcription	Gastric	stomach
37	chr8:11306400-11312200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr8:11306600-11307000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr8:11306600-11307000	Enhancers	Brain Germinal Matrix	brain
40	chr8:11306600-11307400	Enhancers	Esophagus	oesophagus
41	chr8:11306600-11311400	Weak transcription	A549	lung
42	chr8:11306800-11307000	Flanking Active TSS	NHEK	skin
43	chr8:11306800-11307200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr8:11306800-11307200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
45	chr8:11306800-11307200	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr8:11306800-11308600	Weak transcription	GM12878-XiMat	blood
47	chr8:11306800-11308800	Weak transcription	Spleen	Spleen
48	chr8:11306800-11310400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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