Variant report

Variant	rs540742
Chromosome Location	chr1:78585086-78585087
allele	C/T
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:

Extended variants
information (count: 73 )
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];0.83[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];0.89[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];0.83[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];0.91[CHD][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.82[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]
rs554298	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs556170	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.84[TSI][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];0.80[ASN][1000 genomes]
rs566236	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs577978	1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][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];0.89[ASN][1000 genomes]
rs585072	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs585100	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs586333	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs587433	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]
rs593652	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs595384	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[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];0.84[ASN][1000 genomes]
rs599730	0.93[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.94[LWK][hapmap];0.84[TSI][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];0.86[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];0.99[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];0.99[ASN][1000 genomes]
rs624223	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs627654	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap];0.84[TSI][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	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][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];0.94[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6666954	0.85[CHB][hapmap];0.91[CHD][hapmap];0.83[ASN][1000 genomes]
rs668766	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[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];0.83[ASN][1000 genomes]
rs685848	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[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];0.82[TSI][hapmap];0.88[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
rs540742	NEXN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78555400-78608600	Weak transcription	Pancreas	Pancrea
2	chr1:78567000-78586800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:78567600-78607200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:78569800-78592600	Weak transcription	Spleen	Spleen
5	chr1:78570800-78589200	Weak transcription	Right Ventricle	heart
6	chr1:78578200-78594200	Weak transcription	Left Ventricle	heart
7	chr1:78580200-78585600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:78580200-78585800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:78580200-78587400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr1:78580200-78591000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr1:78580200-78598000	Weak transcription	Aorta	Aorta
12	chr1:78580200-78608600	Weak transcription	HepG2	liver
13	chr1:78584000-78585800	Weak transcription	Adipose Nuclei	Adipose
14	chr1:78584200-78630600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr1:78584400-78585400	Weak transcription	Fetal Intestine Large	intestine
16	chr1:78584400-78597200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:78585000-78587000	Strong transcription	Liver	Liver
18	chr1:78585000-78588400	Strong transcription	Fetal Intestine Small	intestine

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