Variant report

Variant	rs587433
Chromosome Location	chr1:78587246-78587247
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78580164..78582715-chr1:78584966..78587634,2	K562	blood:
2	chr1:78469091..78471508-chr1:78586744..78589573,2	K562	blood:

Variant related genes	Relation type
ENSG00000162616	Chromatin interaction
ENSG00000273338	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11162414	0.82[EUR][1000 genomes]
rs1510245	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1848837	0.87[ASN][1000 genomes]
rs478308	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs487316	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs494496	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs507045	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs521029	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs522952	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs523751	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs524031	0.89[CEU][hapmap];0.85[CHB][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs524757	0.82[EUR][1000 genomes]
rs526723	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs531841	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs534283	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs540742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs554298	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs556170	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs557688	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs561300	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs566236	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs577978	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs580426	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs582281	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs582395	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs584660	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs584868	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs585072	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs585100	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs586333	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs593652	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs595384	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs599293	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs599417	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs599730	1.00[CEU][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs600781	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs605659	1.00[CEU][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs609359	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs609390	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs612486	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs614963	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs616332	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs617195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs621524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624223	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs627654	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs627661	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs629947	0.89[EUR][1000 genomes]
rs633227	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs633769	0.86[EUR][1000 genomes]
rs640134	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs642248	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs644359	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs650495	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs651413	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs651897	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs661844	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs663254	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6666954	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs668766	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs674933	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs685393	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs685848	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs687708	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7518152	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7540887	0.83[EUR][1000 genomes]
rs809911	0.87[AMR][1000 genomes]
rs812097	0.94[CEU][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	esv3368799	chr1:78587052-78587424	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs587433	NEXN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78555400-78608600	Weak transcription	Pancreas	Pancrea
2	chr1:78567600-78607200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:78569800-78592600	Weak transcription	Spleen	Spleen
4	chr1:78570800-78589200	Weak transcription	Right Ventricle	heart
5	chr1:78578200-78594200	Weak transcription	Left Ventricle	heart
6	chr1:78580200-78587400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr1:78580200-78591000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr1:78580200-78598000	Weak transcription	Aorta	Aorta
9	chr1:78580200-78608600	Weak transcription	HepG2	liver
10	chr1:78584200-78630600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:78584400-78597200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:78585000-78588400	Strong transcription	Fetal Intestine Small	intestine
13	chr1:78585400-78588600	Strong transcription	Fetal Intestine Large	intestine
14	chr1:78585600-78587400	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr1:78585800-78588600	Strong transcription	Duodenum Mucosa	Duodenum
16	chr1:78586400-78608600	Weak transcription	Colonic Mucosa	Colon
17	chr1:78586800-78587400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:78587000-78592000	Weak transcription	Liver	Liver
19	chr1:78587200-78587600	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr1:78587200-78587600	Enhancers	Osteobl	bone
21	chr1:78587200-78587800	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr1:78587200-78587800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:78587200-78587800	Enhancers	NHDF-Ad	bronchial
24	chr1:78587200-78588200	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr1:78587200-78588400	Enhancers	H1 Cell Line	embryonic stem cell
26	chr1:78587200-78588400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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