Variant report

Variant	rs10058374
Chromosome Location	chr5:43155465-43155466
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:43120824..43123144-chr5:43153299..43156579,5	MCF-7	breast:
2	chr5:43142089..43145048-chr5:43154382..43156409,2	K562	blood:
3	chr5:43149407..43153525-chr5:43154850..43159311,5	K562	blood:
4	chr5:43134921..43137750-chr5:43153839..43155505,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172262	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10044382	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10058350	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10070751	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10074873	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10075647	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10076858	0.90[EUR][1000 genomes]
rs10078527	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs10214190	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10805667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10941607	0.88[JPT][hapmap]
rs10941608	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs10941611	0.86[ASN][1000 genomes]
rs11550287	0.87[JPT][hapmap]
rs11740797	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs11748187	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs12188691	0.87[JPT][hapmap]
rs13173064	0.87[JPT][hapmap]
rs13176429	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1532330	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1532331	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17301375	0.94[JPT][hapmap]
rs316398	0.81[JPT][hapmap]
rs316405	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs316411	0.94[JPT][hapmap]
rs33910990	0.89[ASN][1000 genomes]
rs35953019	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3733839	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs3849699	0.87[JPT][hapmap]
rs4498259	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs479996	0.91[ASN][1000 genomes]
rs4866808	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4866971	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511340	0.86[ASN][1000 genomes]
rs541143	0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs6414900	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6451672	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6451674	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6451675	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs670206	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs6862639	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6864955	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6870418	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6871636	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6876746	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6884303	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6894506	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7701510	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs7709181	0.94[JPT][hapmap]
rs7712046	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7723426	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7729529	0.94[JPT][hapmap]
rs7730004	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[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	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
7	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
8	nsv830274	chr5:43095551-43226087	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	138 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10058374	ZNF131	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43122600-43156200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:43122600-43163400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:43122800-43156400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr5:43122800-43174200	Weak transcription	Colonic Mucosa	Colon
5	chr5:43124000-43183000	Weak transcription	Small Intestine	intestine
6	chr5:43127600-43178000	Strong transcription	Dnd41	blood
7	chr5:43128200-43156000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:43128200-43161000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr5:43128400-43161400	Weak transcription	HSMMtube	muscle
10	chr5:43129000-43161400	Weak transcription	Colon Smooth Muscle	Colon
11	chr5:43130200-43156200	Weak transcription	Gastric	stomach
12	chr5:43131000-43159800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr5:43133000-43161400	Weak transcription	Esophagus	oesophagus
14	chr5:43133200-43161400	Weak transcription	Fetal Brain Male	brain
15	chr5:43135400-43156400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr5:43137200-43163400	Weak transcription	Fetal Kidney	kidney
17	chr5:43137800-43161000	Weak transcription	HSMM	muscle
18	chr5:43138200-43159000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr5:43140800-43155800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr5:43141800-43161400	Weak transcription	HUVEC	blood vessel
21	chr5:43142200-43161400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr5:43143000-43161400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:43143400-43178200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:43143800-43155600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:43143800-43161400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr5:43143800-43161400	Weak transcription	NHEK	skin
27	chr5:43144600-43159600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr5:43145200-43161400	Weak transcription	NH-A	brain
29	chr5:43145400-43156200	Weak transcription	Adipose Nuclei	Adipose
30	chr5:43145400-43161400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr5:43145600-43156000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr5:43146400-43161200	Weak transcription	Liver	Liver
33	chr5:43146600-43161400	Weak transcription	HMEC	breast
34	chr5:43146600-43162200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr5:43147200-43155800	Weak transcription	Fetal Brain Female	brain
36	chr5:43147800-43159600	Strong transcription	Primary T cells from cord blood	blood
37	chr5:43148200-43157000	Strong transcription	Fetal Intestine Large	intestine
38	chr5:43148200-43162200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr5:43148400-43160000	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr5:43148400-43169800	Strong transcription	Hela-S3	cervix
41	chr5:43149800-43161000	Strong transcription	Fetal Thymus	thymus
42	chr5:43150200-43159600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr5:43150200-43161200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr5:43150600-43157000	Strong transcription	Fetal Stomach	stomach
45	chr5:43150600-43167400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr5:43150800-43155600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr5:43151000-43161400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr5:43151200-43160600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr5:43151400-43156000	Weak transcription	Fetal Lung	lung
50	chr5:43151400-43161000	Weak transcription	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links