Variant report

Variant	rs2095376
Chromosome Location	chr6:150189174-150189175
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr6:150189080-150189876	K562	blood:	n/a	n/a
2	BACH1	chr6:150188976-150190762	K562	blood:	n/a	n/a
3	POLR2A	chr6:150189094-150190357	MCF10A-Er-Src	breast:	n/a	n/a
4	CBX3	chr6:150188243-150191119	K562	blood:	n/a	n/a
5	CEBPB	chr6:150189018-150189739	Hela-S3	cervix:	n/a	n/a
6	TBL1XR1	chr6:150189038-150189191	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:150187701..150190612-chr6:150206560..150208609,2	K562	blood:
2	chr6:150185041..150187109-chr6:150187854..150189686,2	K562	blood:
3	chr6:150184661..150189239-chr6:150198084..150201371,4	MCF-7	breast:
4	chr6:150182195..150187725-chr6:150188544..150196234,11	MCF-7	breast:
5	chr2:174828821..174830614-chr6:150186810..150189334,2	MCF-7	breast:
6	chr6:150188984..150191579-chr6:150203817..150206821,3	MCF-7	breast:
7	chr6:150188453..150191090-chr6:150209708..150211958,2	K562	blood:

No data

Variant related genes	Relation type
LRP11	TF binding region
ENSG00000268592	Chromatin interaction
ENSG00000120256	Chromatin interaction
ENSG00000223701	Chromatin interaction
ENSG00000172845	Chromatin interaction
ENSG00000217733	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1334510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1889471	0.82[EUR][1000 genomes]
rs2342767	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2342768	0.81[EUR][1000 genomes]
rs2342769	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2342770	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3823021	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4458704	1.00[CEU][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4869763	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4869764	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4870116	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6557133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6933882	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6935829	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6939761	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7740145	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7742692	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7742993	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7744821	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7747435	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7747457	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7753544	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7756850	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7757972	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7757984	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7758020	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7758033	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7763719	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7763849	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7764376	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7767588	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7767592	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7768626	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7768665	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7769118	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7771014	0.89[EUR][1000 genomes]
rs7774787	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9322225	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9322228	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9371215	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9371223	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9371504	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9371505	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9371533	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9371542	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9371544	0.92[CEU][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9383577	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9383584	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9383912	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9383913	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9383914	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9383921	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9383940	1.00[CEU][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9397058	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9397398	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9397420	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9397434	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9397438	0.85[JPT][hapmap]
rs9478192	0.86[EUR][1000 genomes]
rs9968871	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9969044	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9986576	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh 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	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs2095376	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs2095376	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs2095376	RP11-350J20.5	cis	Artery Tibial	GTEx
rs2095376	RP11-350J20.9	cis	Heart Left Ventricle	GTEx
rs2095376	RAET1E	cis	Nerve Tibial	GTEx
rs2095376	LRP11	cis	Skin Sun Exposed Lower leg	GTEx
rs2095376	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs2095376	RP11-350J20.9	cis	Skin Sun Exposed Lower leg	GTEx
rs2095376	LRP11	cis	Adipose Subcutaneous	GTEx
rs2095376	RAET1G	cis	Thyroid	GTEx
rs2095376	RAET1G	cis	Artery Tibial	GTEx
rs2095376	RP11-350J20.5	cis	Thyroid	GTEx
rs2095376	RP11-350J20.5	cis	Esophagus Mucosa	GTEx
rs2095376	RP11-350J20.9	cis	lung	GTEx
rs2095376	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs2095376	NUP43	cis	Whole Blood	GTEx
rs2095376	RP11-350J20.5	cis	lung	GTEx
rs2095376	RP11-350J20.9	cis	Muscle Skeletal	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150185800-150189200	Weak transcription	Gastric	stomach
2	chr6:150186000-150189200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:150186200-150189200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:150186200-150189200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:150186200-150189200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:150186200-150189200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:150186200-150189200	Weak transcription	NHEK	skin
8	chr6:150186200-150189400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:150186200-150189600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr6:150186200-150189600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:150186200-150189800	Weak transcription	Ovary	ovary
12	chr6:150186200-150190000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:150186200-150194400	Weak transcription	Pancreas	Pancrea
14	chr6:150186400-150189400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr6:150186400-150189400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:150186600-150189400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:150186600-150189400	Weak transcription	Liver	Liver
18	chr6:150188000-150189800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:150188800-150189800	Flanking Active TSS	K562	blood
20	chr6:150188800-150190000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr6:150188800-150190200	Enhancers	HMEC	breast
22	chr6:150188800-150190400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:150189000-150189600	Enhancers	HepG2	liver
24	chr6:150189000-150189600	Enhancers	NHLF	lung
25	chr6:150189000-150189800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:150189000-150190000	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr6:150189000-150190000	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr6:150189000-150190000	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr6:150189000-150190000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:150189000-150190000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:150189000-150190000	Enhancers	A549	lung
32	chr6:150189000-150190000	Enhancers	NHDF-Ad	bronchial
33	chr6:150189000-150190200	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr6:150189000-150190200	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr6:150189000-150190200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:150189000-150190200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:150189000-150190400	Enhancers	H1 Cell Line	embryonic stem cell
38	chr6:150189000-150190400	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr6:150189000-150190400	Enhancers	Hela-S3	cervix

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