Variant report

Variant	rs58909712
Chromosome Location	chr4:76910813-76910814
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:76859777..76862033-chr4:76910435..76912057,2	K562	blood:
2	chr4:76861625..76863720-chr4:76909476..76912300,3	MCF-7	breast:
3	chr4:76889181..76890781-chr4:76908740..76910995,2	K562	blood:
4	chr4:76910728..76913331-chr4:77052548..77055482,2	MCF-7	breast:
5	chr4:76910224..76911940-chr4:76940902..76942598,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138744	Chromatin interaction
ENSG00000138750	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10222911	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1050176	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10856871	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097192	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12500200	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12511861	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1554015	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17001275	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17001284	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1910907	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869461	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28703679	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733236	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859412	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55964684	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56039229	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56105413	0.96[EUR][1000 genomes]
rs56316945	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59559903	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61279846	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532084	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66477189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67210456	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67297326	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67413521	0.85[ASN][1000 genomes]
rs67687266	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6828744	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6834291	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847716	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857358	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72651379	0.88[EUR][1000 genomes]
rs72651387	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7349626	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7670156	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7671125	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7696286	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1004627	chr4:76793910-76999584	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58909712	ASAHL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76887200-76911000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:76900200-76911000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:76902000-76911000	Weak transcription	Aorta	Aorta
4	chr4:76902200-76911000	Weak transcription	Gastric	stomach
5	chr4:76902200-76911000	Weak transcription	Pancreas	Pancrea
6	chr4:76902200-76911200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:76902200-76911200	Weak transcription	Esophagus	oesophagus
8	chr4:76902600-76911000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr4:76903800-76911000	Weak transcription	Placenta	Placenta
10	chr4:76908200-76911000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:76908200-76911200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:76909000-76911000	Enhancers	Primary B cells from peripheral blood	blood
13	chr4:76910000-76911000	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr4:76910000-76911200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:76910000-76911200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:76910000-76911200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr4:76910000-76911200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr4:76910000-76911200	Enhancers	Stomach Mucosa	stomach
19	chr4:76910000-76911200	Flanking Active TSS	Dnd41	blood
20	chr4:76910000-76911200	Flanking Active TSS	HMEC	breast
21	chr4:76910000-76911400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:76910200-76911000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr4:76910200-76911000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr4:76910200-76911000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr4:76910200-76911000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:76910200-76911000	Enhancers	Fetal Thymus	thymus
27	chr4:76910200-76911000	Weak transcription	Left Ventricle	heart
28	chr4:76910200-76911000	Enhancers	Spleen	Spleen
29	chr4:76910200-76911000	Flanking Active TSS	NHDF-Ad	bronchial
30	chr4:76910200-76911000	Flanking Active TSS	NHEK	skin
31	chr4:76910200-76911200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:76910200-76911200	Flanking Active TSS	Colon Smooth Muscle	Colon
33	chr4:76910200-76911200	Enhancers	Placenta Amnion	Placenta Amnion
34	chr4:76910200-76911400	Flanking Active TSS	Liver	Liver
35	chr4:76910200-76911400	Flanking Active TSS	Osteobl	bone
36	chr4:76910200-76911800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:76910200-76912600	Active TSS	Right Ventricle	heart
38	chr4:76910400-76911000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr4:76910400-76911000	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr4:76910400-76911200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr4:76910400-76911200	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr4:76910400-76911200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr4:76910400-76911200	Flanking Active TSS	NH-A	brain
44	chr4:76910400-76911400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr4:76910400-76911400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:76910400-76912200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr4:76910400-76912600	Active TSS	H1 Cell Line	embryonic stem cell
48	chr4:76910400-76912600	Active TSS	NHLF	lung
49	chr4:76910400-76912800	Active TSS	A549	lung
50	chr4:76910600-76911000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links