Variant report

Variant	rs13179406
Chromosome Location	chr5:179453077-179453078
allele	A/C
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	chr5:179452407..179455273-chr5:179474700..179476534,2	K562	blood:
2	chr5:179452184..179453736-chr5:179495746..179497610,2	MCF-7	breast:
3	chr5:179451853..179453889-chr5:179463627..179465589,2	MCF-7	breast:
4	chr5:179449447..179452303-chr5:179452707..179456164,4	K562	blood:
5	chr5:179435243..179436758-chr5:179452020..179454340,2	K562	blood:
6	chr5:179246226..179248530-chr5:179451995..179454852,2	MCF-7	breast:
7	chr5:179449447..179452812-chr5:179452843..179455621,3	K562	blood:
8	chr5:179451009..179454455-chr5:179516109..179519066,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000161011	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1102191	0.88[AFR][1000 genomes]
rs12519642	0.96[AFR][1000 genomes]
rs12656814	0.91[AFR][1000 genomes]
rs13161895	0.92[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs13166286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17079966	0.93[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs17079968	0.96[AFR][1000 genomes]
rs248318	0.93[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs248320	0.93[CEU][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs27012	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs27018	0.93[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs34027780	0.91[AFR][1000 genomes]
rs34603792	0.96[AFR][1000 genomes]
rs34674199	0.91[AFR][1000 genomes]
rs35135297	0.91[AFR][1000 genomes]
rs35592104	0.96[AFR][1000 genomes]
rs35608303	0.91[AFR][1000 genomes]
rs35973843	0.91[AFR][1000 genomes]
rs35988237	0.91[AFR][1000 genomes]
rs3719	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs379655	0.96[AFR][1000 genomes]
rs3797763	0.93[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs3797764	0.93[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs394616	0.96[AFR][1000 genomes]
rs4129403	0.93[CEU][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs4235504	0.92[CEU][hapmap]
rs438050	0.88[AFR][1000 genomes]
rs4389651	0.96[AFR][1000 genomes]
rs442181	0.96[AFR][1000 genomes]
rs4700853	0.91[AFR][1000 genomes]
rs594202	0.96[AFR][1000 genomes]
rs6873781	0.93[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs6873994	0.93[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs6876648	0.96[AFR][1000 genomes]
rs71613436	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71613437	0.91[AFR][1000 genomes]
rs71613438	0.91[AFR][1000 genomes]
rs857187	0.96[AFR][1000 genomes]
rs857188	0.96[AFR][1000 genomes]
rs864482	0.93[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer 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	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
7	nsv1024592	chr5:179443133-179510642	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13179406	LMAN2	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179396600-179461800	Weak transcription	HSMM	muscle
2	chr5:179405200-179453400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:179421800-179462400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr5:179428600-179462200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr5:179429800-179462400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr5:179429800-179463000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr5:179429800-179463200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:179429800-179482600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr5:179430600-179462400	Weak transcription	HepG2	liver
10	chr5:179435400-179453400	Weak transcription	Right Atrium	heart
11	chr5:179435800-179454600	Weak transcription	K562	blood
12	chr5:179437600-179462600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr5:179438000-179466400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr5:179439600-179453400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr5:179440000-179453400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:179440200-179457600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:179440200-179462600	Weak transcription	Fetal Intestine Large	intestine
18	chr5:179440600-179462400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr5:179444200-179453400	Weak transcription	Brain Angular Gyrus	brain
20	chr5:179446000-179462200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr5:179447600-179453400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr5:179447600-179453400	Weak transcription	Pancreas	Pancrea
23	chr5:179447600-179454000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr5:179447600-179454000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:179447600-179454000	Weak transcription	Aorta	Aorta
26	chr5:179447600-179454000	Weak transcription	Fetal Lung	lung
27	chr5:179447600-179454000	Weak transcription	Gastric	stomach
28	chr5:179447600-179459600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr5:179447600-179462400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr5:179447600-179463200	Weak transcription	Esophagus	oesophagus
31	chr5:179447600-179463200	Weak transcription	Lung	lung
32	chr5:179447600-179463200	Weak transcription	HSMMtube	muscle
33	chr5:179447800-179453400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr5:179447800-179453400	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr5:179447800-179453400	Weak transcription	Left Ventricle	heart
36	chr5:179447800-179454000	Weak transcription	Spleen	Spleen
37	chr5:179447800-179454400	Weak transcription	Fetal Kidney	kidney
38	chr5:179447800-179454600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr5:179447800-179461600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr5:179447800-179461600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr5:179447800-179462400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr5:179447800-179462400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr5:179447800-179463000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr5:179447800-179463000	Weak transcription	Stomach Smooth Muscle	stomach
45	chr5:179447800-179463200	Weak transcription	Ovary	ovary
46	chr5:179447800-179466800	Weak transcription	Hela-S3	cervix
47	chr5:179448000-179453400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr5:179448000-179453400	Weak transcription	Right Ventricle	heart
49	chr5:179448000-179458600	Weak transcription	A549	lung
50	chr5:179448200-179457400	Weak transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links