Variant report

Variant	rs13180496
Chromosome Location	chr5:43079509-43079510
allele	A/G
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:43076850..43080824-chr5:43095095..43097959,3	K562	blood:
2	chr5:43064084..43067550-chr5:43078296..43080373,3	K562	blood:
3	chr5:43077895..43080643-chr5:43081043..43085199,4	MCF-7	breast:
4	chr5:43064084..43066888-chr5:43078296..43080622,3	K562	blood:
5	chr5:43078366..43081197-chr5:43092344..43095133,2	K562	blood:
6	chr5:43074312..43077357-chr5:43077925..43083201,8	K562	blood:
7	chr5:43078520..43080720-chr5:43120036..43121889,2	MCF-7	breast:
8	chr5:43078395..43080748-chr5:43104013..43106057,2	K562	blood:
9	chr5:43079311..43081583-chr5:43091403..43093929,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000177738	Chromatin interaction
ENSG00000172262	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1001717	0.92[CEU][hapmap]
rs10045847	1.00[CHB][hapmap]
rs10045863	1.00[CHB][hapmap]
rs10072083	1.00[CHB][hapmap]
rs1084520	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11550288	1.00[ASN][1000 genomes]
rs13156403	1.00[ASN][1000 genomes]
rs13156729	1.00[ASN][1000 genomes]
rs13158147	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13160133	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13163892	0.91[CEU][hapmap]
rs13164183	0.91[CEU][hapmap]
rs13167375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13167991	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13169195	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13170322	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13170959	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13171192	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13171253	0.92[CEU][hapmap]
rs13174226	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs13175754	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13176080	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13186091	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13186549	0.86[CEU][hapmap]
rs16873177	0.85[CEU][hapmap]
rs17242731	0.92[CEU][hapmap]
rs17242995	0.91[CEU][hapmap]
rs17243023	0.92[CEU][hapmap]
rs17243086	0.85[CEU][hapmap]
rs17243515	1.00[CEU][hapmap]
rs17302596	0.85[CEU][hapmap]
rs17302931	1.00[CEU][hapmap]
rs17303482	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2085100	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34157680	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34215864	1.00[ASN][1000 genomes]
rs34345245	1.00[ASN][1000 genomes]
rs34517361	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34735159	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34810824	1.00[ASN][1000 genomes]
rs34967469	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35030460	1.00[ASN][1000 genomes]
rs35197809	1.00[ASN][1000 genomes]
rs35322710	1.00[ASN][1000 genomes]
rs35334781	1.00[ASN][1000 genomes]
rs35397154	1.00[CEU][hapmap]
rs35484387	1.00[ASN][1000 genomes]
rs35594379	1.00[ASN][1000 genomes]
rs35756781	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35764948	1.00[ASN][1000 genomes]
rs36048737	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36122053	1.00[ASN][1000 genomes]
rs3752831	1.00[CEU][hapmap]
rs3752832	0.92[CEU][hapmap]
rs3797306	0.92[CEU][hapmap]
rs3797307	0.92[CEU][hapmap]
rs3797308	0.85[CEU][hapmap]
rs3797309	0.92[CEU][hapmap]
rs503965	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs505573	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs614386	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs632730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6863953	1.00[CHB][hapmap]
rs71627567	1.00[ASN][1000 genomes]
rs71627568	0.87[EUR][1000 genomes]
rs878234	1.00[CEU][hapmap];1.00[CHB][hapmap]

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	nsv870299	chr5:43053679-43107880	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13180496	ZNF131	cis	Artery Tibial	GTEx
rs13180496	ZNF131	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43068600-43082600	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr5:43069000-43081400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:43069400-43082800	Weak transcription	Colonic Mucosa	Colon
4	chr5:43069400-43087400	Weak transcription	Stomach Mucosa	stomach
5	chr5:43069600-43080400	Strong transcription	Fetal Muscle Trunk	muscle
6	chr5:43069600-43080400	Strong transcription	Fetal Muscle Leg	muscle
7	chr5:43070000-43105400	Weak transcription	HSMMtube	muscle
8	chr5:43071400-43084400	Weak transcription	Fetal Kidney	kidney
9	chr5:43071600-43080800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr5:43071600-43083800	Weak transcription	HepG2	liver
11	chr5:43071600-43084200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr5:43071800-43079600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr5:43071800-43080000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr5:43071800-43080000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr5:43071800-43080200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr5:43071800-43080200	Weak transcription	Gastric	stomach
17	chr5:43071800-43081400	Weak transcription	Fetal Brain Male	brain
18	chr5:43071800-43081800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr5:43071800-43081800	Weak transcription	Hela-S3	cervix
20	chr5:43071800-43082000	Weak transcription	HMEC	breast
21	chr5:43071800-43082800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr5:43071800-43083000	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr5:43071800-43084800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:43071800-43091000	Weak transcription	Colon Smooth Muscle	Colon
25	chr5:43071800-43091600	Weak transcription	Ovary	ovary
26	chr5:43071800-43096000	Weak transcription	Aorta	Aorta
27	chr5:43071800-43098400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr5:43071800-43101600	Weak transcription	Esophagus	oesophagus
29	chr5:43071800-43105400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr5:43072000-43079800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr5:43072000-43080600	Weak transcription	Brain Substantia Nigra	brain
32	chr5:43072000-43081800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr5:43072400-43104200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr5:43073000-43080400	Weak transcription	HSMM	muscle
35	chr5:43073400-43079800	Weak transcription	Primary B cells from peripheral blood	blood
36	chr5:43073400-43080400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:43074000-43082600	Strong transcription	Fetal Thymus	thymus
38	chr5:43074400-43082400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr5:43074800-43082200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:43075000-43081400	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr5:43075200-43081600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr5:43075400-43080000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr5:43075400-43082600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr5:43075400-43084400	Weak transcription	Fetal Lung	lung
45	chr5:43075600-43081200	Strong transcription	Dnd41	blood
46	chr5:43075600-43096600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr5:43075600-43101600	Weak transcription	Left Ventricle	heart
48	chr5:43075600-43105000	Weak transcription	NHLF	lung
49	chr5:43075600-43105400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr5:43075600-43105400	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links