Variant report

Variant	rs541143
Chromosome Location	chr5:43123079-43123080
allele	C/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:43120068..43123427-chr5:43312084..43315058,4	MCF-7	breast:
2	chr5:43121173..43123733-chr5:43225214..43227134,2	MCF-7	breast:
3	chr5:43121048..43123106-chr5:43555521..43557723,3	MCF-7	breast:
4	chr5:43006330..43010322-chr5:43119527..43123237,8	MCF-7	breast:
5	chr5:43063463..43067998-chr5:43119333..43125586,12	K562	blood:
6	chr5:43064995..43071284-chr5:43119667..43123996,15	MCF-7	breast:
7	chr5:43120976..43123140-chr5:43225337..43226938,2	MCF-7	breast:
8	chr5:43062052..43069089-chr5:43119705..43123366,12	MCF-7	breast:
9	chr5:43063723..43068505-chr5:43119531..43125230,17	K562	blood:
10	chr5:43120765..43125898-chr5:43482451..43485837,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000249492	Chromatin interaction
ENSG00000177738	Chromatin interaction
ENSG00000151881	Chromatin interaction
ENSG00000172262	Chromatin interaction
ENSG00000249888	Chromatin interaction
ENSG00000112972	Chromatin interaction
ENSG00000271788	Chromatin interaction
ENSG00000172239	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10044382	0.91[ASN][1000 genomes]
rs10058350	0.93[ASN][1000 genomes]
rs10058374	0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs10070751	0.91[ASN][1000 genomes]
rs10074873	0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs10075647	0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs10078527	0.87[JPT][hapmap]
rs10214190	0.89[ASN][1000 genomes]
rs10805667	0.82[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs10941607	0.87[JPT][hapmap]
rs10941608	0.87[JPT][hapmap]
rs10941611	0.80[ASN][1000 genomes]
rs11550287	0.86[JPT][hapmap]
rs11740797	0.93[JPT][hapmap]
rs11748187	0.94[JPT][hapmap]
rs12188691	0.86[JPT][hapmap]
rs13173064	0.86[JPT][hapmap]
rs13176429	0.93[ASN][1000 genomes]
rs13665	0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs1532330	0.92[ASN][1000 genomes]
rs1532331	0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs1618891	0.96[YRI][hapmap]
rs1624415	0.84[YRI][hapmap]
rs17301375	0.94[JPT][hapmap]
rs2548353	0.81[YRI][hapmap]
rs2548356	0.82[YRI][hapmap]
rs316398	0.80[JPT][hapmap]
rs316405	0.93[JPT][hapmap]
rs316411	0.93[JPT][hapmap]
rs33910990	0.83[ASN][1000 genomes]
rs35953019	0.93[JPT][hapmap]
rs3733839	0.94[JPT][hapmap]
rs3849698	0.86[JPT][hapmap]
rs3849699	0.86[JPT][hapmap]
rs4498259	0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs479996	0.91[ASN][1000 genomes]
rs4866808	0.91[ASN][1000 genomes]
rs4866971	0.93[ASN][1000 genomes]
rs511340	0.86[ASN][1000 genomes]
rs512921	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs521649	0.80[AFR][1000 genomes]
rs567884	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs6414900	0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs6451672	0.84[ASN][1000 genomes]
rs6451674	0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs6451675	0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs670206	0.94[JPT][hapmap]
rs6862639	0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs6864955	0.91[ASN][1000 genomes]
rs6870418	0.92[ASN][1000 genomes]
rs6871636	0.93[JPT][hapmap]
rs6876746	0.91[ASN][1000 genomes]
rs6884303	0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs6892422	0.81[YRI][hapmap]
rs6894506	0.91[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs7701510	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7709181	0.93[JPT][hapmap]
rs7712046	0.93[ASN][1000 genomes]
rs7723426	0.86[ASN][1000 genomes]
rs7729529	0.94[JPT][hapmap]
rs7730004	0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs782978	0.88[YRI][hapmap]
rs782984	0.80[YRI][hapmap]
rs903391	0.89[YRI][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	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
rs541143	ZNF131	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43120600-43123200	Active TSS	H1 Cell Line	embryonic stem cell
2	chr5:43120600-43123200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:43120600-43123200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr5:43120600-43123400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:43120600-43123400	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr5:43120600-43123600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr5:43120800-43123800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr5:43120800-43124000	Active TSS	Psoas Muscle	Psoas
9	chr5:43121000-43123400	Active TSS	GM12878-XiMat	blood
10	chr5:43121800-43123200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr5:43121800-43123400	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr5:43122000-43123200	Active TSS	Right Atrium	heart
13	chr5:43122000-43123400	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr5:43122000-43123800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:43122200-43123200	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr5:43122200-43123400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:43122200-43123800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr5:43122200-43123800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr5:43122400-43123200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr5:43122400-43123200	Flanking Active TSS	Colon Smooth Muscle	Colon
21	chr5:43122400-43123200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr5:43122400-43123400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr5:43122400-43123400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr5:43122400-43123400	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr5:43122400-43123400	Flanking Active TSS	Fetal Lung	lung
26	chr5:43122400-43123400	Flanking Active TSS	HMEC	breast
27	chr5:43122400-43123400	Flanking Active TSS	HUVEC	blood vessel
28	chr5:43122400-43123400	Flanking Active TSS	NHDF-Ad	bronchial
29	chr5:43122400-43123600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:43122400-43123600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr5:43122400-43123600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr5:43122400-43123600	Flanking Active TSS	NHEK	skin
33	chr5:43122400-43124000	Flanking Active TSS	Brain Germinal Matrix	brain
34	chr5:43122400-43124200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr5:43122400-43124200	Transcr. at gene 5' and 3'	K562	blood
36	chr5:43122400-43125000	Transcr. at gene 5' and 3'	Dnd41	blood
37	chr5:43122600-43123200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr5:43122600-43123200	Enhancers	Brain Substantia Nigra	brain
39	chr5:43122600-43123200	Flanking Active TSS	Fetal Heart	heart
40	chr5:43122600-43123200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr5:43122600-43123400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr5:43122600-43123400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr5:43122600-43123400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr5:43122600-43123400	Flanking Active TSS	Fetal Brain Male	brain
45	chr5:43122600-43123600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr5:43122600-43123600	Weak transcription	Placenta	Placenta
47	chr5:43122600-43123800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr5:43122600-43123800	Enhancers	Liver	Liver
49	chr5:43122600-43124000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr5:43122600-43124000	Enhancers	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links