Variant report

Variant	rs812097
Chromosome Location	chr1:78566234-78566235
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:78557581..78562861-chr1:78563464..78569701,7	K562	blood:
2	chr1:78544325..78546511-chr1:78564986..78567853,2	MCF-7	breast:
3	chr1:78467852..78476620-chr1:78566212..78581721,30	K562	blood:
4	chr1:78468395..78470223-chr1:78565706..78567712,2	K562	blood:
5	chr1:78565458..78567789-chr1:78569626..78572269,2	K562	blood:

Variant related genes	Relation type
ENSG00000202263	Chromatin interaction
ENSG00000273338	Chromatin interaction
ENSG00000162616	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs11162412	0.87[AFR][1000 genomes]
rs12067638	0.90[LWK][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs1510245	0.89[EUR][1000 genomes]
rs1770307	0.81[CEU][hapmap]
rs3790592	0.93[LWK][hapmap];0.93[MKK][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes]
rs481199	0.90[AFR][1000 genomes]
rs483760	0.93[LWK][hapmap];0.84[MKK][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes]
rs485005	0.90[AFR][1000 genomes]
rs494496	0.82[EUR][1000 genomes]
rs5001390	0.84[AFR][1000 genomes]
rs501935	0.87[AFR][1000 genomes]
rs505301	0.93[LWK][hapmap];0.83[MKK][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes]
rs507045	0.89[EUR][1000 genomes]
rs515662	0.86[AFR][1000 genomes]
rs521029	0.82[EUR][1000 genomes]
rs522952	0.89[EUR][1000 genomes]
rs523751	0.82[EUR][1000 genomes]
rs524031	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs526723	0.82[EUR][1000 genomes]
rs531841	0.84[EUR][1000 genomes]
rs534283	0.89[EUR][1000 genomes]
rs539228	0.90[AFR][1000 genomes]
rs540742	0.94[CEU][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs554298	0.82[EUR][1000 genomes]
rs556170	0.94[CEU][hapmap]
rs557688	0.82[EUR][1000 genomes]
rs561300	0.88[EUR][1000 genomes]
rs565164	0.90[AFR][1000 genomes]
rs566236	0.88[EUR][1000 genomes]
rs571255	0.93[LWK][hapmap];0.93[MKK][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes]
rs571988	0.93[LWK][hapmap];0.93[MKK][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes]
rs577978	0.94[CEU][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs580426	0.82[EUR][1000 genomes]
rs582281	0.82[EUR][1000 genomes]
rs582395	0.82[EUR][1000 genomes]
rs584660	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs585072	0.89[EUR][1000 genomes]
rs585100	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs586333	0.89[EUR][1000 genomes]
rs586680	0.86[AFR][1000 genomes]
rs587143	0.93[LWK][hapmap];0.93[MKK][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes]
rs587433	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs593652	0.84[EUR][1000 genomes]
rs594852	0.86[AFR][1000 genomes]
rs595384	0.89[EUR][1000 genomes]
rs599417	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs599730	0.94[CEU][hapmap]
rs600742	0.90[AFR][1000 genomes]
rs600781	0.82[EUR][1000 genomes]
rs605659	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs609359	0.82[EUR][1000 genomes]
rs609390	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs610501	0.82[AFR][1000 genomes]
rs611820	0.85[AFR][1000 genomes]
rs612486	0.82[EUR][1000 genomes]
rs614963	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs616332	0.88[EUR][1000 genomes]
rs617195	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs621524	0.88[EUR][1000 genomes]
rs627654	0.94[CEU][hapmap]
rs627661	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs629947	0.81[EUR][1000 genomes]
rs630245	0.93[LWK][hapmap];0.93[MKK][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes]
rs630640	0.88[YRI][hapmap];0.90[AFR][1000 genomes]
rs631045	0.93[LWK][hapmap];0.93[MKK][hapmap];0.87[YRI][hapmap]
rs633227	0.84[EUR][1000 genomes]
rs638668	0.86[AFR][1000 genomes]
rs639677	0.88[YRI][hapmap];0.90[AFR][1000 genomes]
rs642248	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs643512	0.90[AFR][1000 genomes]
rs644359	0.80[EUR][1000 genomes]
rs650495	0.88[EUR][1000 genomes]
rs651897	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs654185	0.88[YRI][hapmap];0.85[AFR][1000 genomes]
rs657954	0.93[LWK][hapmap];0.84[MKK][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes]
rs661844	0.89[EUR][1000 genomes]
rs663254	0.94[CEU][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs664448	0.88[YRI][hapmap];0.90[AFR][1000 genomes]
rs6669039	0.90[LWK][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes]
rs666995	0.84[AFR][1000 genomes]
rs6684364	0.95[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs6688346	0.87[AFR][1000 genomes]
rs674933	0.80[EUR][1000 genomes]
rs675799	0.81[CEU][hapmap]
rs677640	0.90[AFR][1000 genomes]
rs685393	0.89[EUR][1000 genomes]
rs685848	0.86[EUR][1000 genomes]
rs686716	0.88[YRI][hapmap];0.90[AFR][1000 genomes]
rs687708	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs7518152	0.82[EUR][1000 genomes]
rs7540887	0.86[AMR][1000 genomes];0.84[EUR][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
rs812097	NEXN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78535000-78566800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:78546600-78579800	Weak transcription	Liver	Liver
3	chr1:78553400-78567000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:78554800-78579800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:78555400-78608600	Weak transcription	Pancreas	Pancrea
6	chr1:78557800-78569200	Weak transcription	Fetal Intestine Small	intestine
7	chr1:78558600-78582800	Weak transcription	Fetal Intestine Large	intestine
8	chr1:78560800-78566800	Weak transcription	Stomach Mucosa	stomach
9	chr1:78562000-78566400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:78562000-78566600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr1:78562400-78566800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:78562600-78567000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:78562800-78566600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:78562800-78566800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:78562800-78566800	Weak transcription	Right Atrium	heart
16	chr1:78563000-78566600	Weak transcription	NHEK	skin
17	chr1:78563200-78566800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:78563200-78567000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:78563400-78566400	Weak transcription	Psoas Muscle	Psoas
20	chr1:78563400-78566800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:78563400-78566800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:78563400-78566800	Weak transcription	HMEC	breast
23	chr1:78563400-78568600	Weak transcription	Left Ventricle	heart
24	chr1:78563400-78569200	Weak transcription	Aorta	Aorta
25	chr1:78563600-78566600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:78563600-78566600	Weak transcription	NHLF	lung
27	chr1:78563600-78566800	Weak transcription	Fetal Muscle Leg	muscle
28	chr1:78563600-78569200	Weak transcription	Right Ventricle	heart
29	chr1:78564400-78575800	Weak transcription	HepG2	liver
30	chr1:78564800-78570800	Enhancers	HUVEC	blood vessel
31	chr1:78565400-78567400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:78565600-78566800	Enhancers	Muscle Satellite Cultured Cells	--
33	chr1:78565600-78567600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:78565800-78570800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:78565800-78570800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:78565800-78570800	Enhancers	NHDF-Ad	bronchial
37	chr1:78565800-78570800	Enhancers	Osteobl	bone
38	chr1:78565800-78571400	Enhancers	HSMM	muscle
39	chr1:78566000-78570800	Enhancers	HSMMtube	muscle
40	chr1:78566200-78566800	Enhancers	Fetal Heart	heart
41	chr1:78566200-78567000	Enhancers	Small Intestine	intestine
42	chr1:78566200-78567400	Enhancers	NH-A	brain

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