Variant report

Variant	rs6688346
Chromosome Location	chr1:78537318-78537319
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:78534641..78538084-chr1:78538744..78543341,4	K562	blood:
2	chr1:78467630..78472853-chr1:78532033..78539967,9	K562	blood:
3	chr1:78468499..78472700-chr1:78534079..78541186,10	K562	blood:

Variant related genes	Relation type
ENSG00000273338	Chromatin interaction
ENSG00000162616	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11162412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12067638	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs3790592	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs481199	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs483760	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs485005	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5001390	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs501935	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs505301	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515662	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs539228	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs565164	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs571255	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs571988	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs586680	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs587143	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs594852	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs598988	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs600742	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs610501	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs611820	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs630245	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs630640	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs638668	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs639677	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs640935	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs643512	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs654185	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs657954	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs658780	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs664448	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6669039	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs666995	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677640	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs686716	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7539956	0.82[AMR][1000 genomes]
rs812097	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv870608	chr1:78520822-78594286	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6688346	NEXN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78534600-78537400	Enhancers	Muscle Satellite Cultured Cells	--
2	chr1:78534600-78538200	Enhancers	HSMM	muscle
3	chr1:78534600-78542000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:78534800-78537400	Weak transcription	Left Ventricle	heart
5	chr1:78534800-78538200	Enhancers	NH-A	brain
6	chr1:78534800-78547200	Weak transcription	Fetal Intestine Large	intestine
7	chr1:78534800-78552400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:78535000-78537400	Weak transcription	Adipose Nuclei	Adipose
9	chr1:78535000-78538200	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr1:78535000-78544000	Weak transcription	HepG2	liver
11	chr1:78535000-78566800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:78535200-78538200	Enhancers	NHLF	lung
13	chr1:78535200-78541400	Weak transcription	Fetal Heart	heart
14	chr1:78535200-78554600	Weak transcription	Fetal Intestine Small	intestine
15	chr1:78535400-78538200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:78535400-78538200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:78535400-78538400	Enhancers	Osteobl	bone
18	chr1:78535600-78538200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:78535600-78538200	Enhancers	NHDF-Ad	bronchial
20	chr1:78535600-78538200	Enhancers	NHEK	skin
21	chr1:78535600-78538400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:78535600-78541200	Enhancers	HUVEC	blood vessel
23	chr1:78535800-78538200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:78536000-78538200	Enhancers	HMEC	breast
25	chr1:78536000-78538400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:78536200-78537400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:78536200-78537400	Weak transcription	Hela-S3	cervix
28	chr1:78536400-78537400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:78536400-78537400	Weak transcription	HSMMtube	muscle
30	chr1:78536600-78538000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:78537000-78540000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:78537200-78538200	Enhancers	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links