Variant report

Variant	rs633227
Chromosome Location	chr1:78599369-78599370
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:78469789..78471628-chr1:78598179..78600096,2	K562	blood:
2	chr1:78594062..78596652-chr1:78598664..78601035,2	K562	blood:
3	chr1:78598713..78601395-chr1:78602545..78604596,2	K562	blood:
4	chr1:78598713..78600693-chr1:78601161..78604045,2	K562	blood:

Variant related genes	Relation type
ENSG00000273338	Chromatin interaction
ENSG00000162616	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1407747	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1407748	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1510245	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1625234	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1770307	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4258184	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4285658	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4650607	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs478308	0.82[EUR][1000 genomes]
rs487316	0.80[EUR][1000 genomes]
rs488469	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs494496	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs501774	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs507045	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs513245	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs513977	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs521029	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs522952	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs523751	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs524757	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs526723	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs531841	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs534283	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs540742	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs554298	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs556170	0.81[EUR][1000 genomes]
rs557688	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs558643	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs561289	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs561300	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs566236	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs577978	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580426	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs582281	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs582395	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs582795	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs584660	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs584868	0.82[EUR][1000 genomes]
rs585072	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs585100	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs586333	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs587433	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs591343	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs593652	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs595384	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs597063	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs597272	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs599293	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs599417	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs599730	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs600781	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs605659	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs609359	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs609390	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs610508	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs612486	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs614836	0.88[AMR][1000 genomes]
rs614963	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs616332	0.92[EUR][1000 genomes]
rs617195	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs618063	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs618551	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs618581	0.81[ASN][1000 genomes]
rs618593	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs621524	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs624223	0.81[EUR][1000 genomes]
rs624766	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs627654	0.81[EUR][1000 genomes]
rs627661	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs629947	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs633664	0.82[ASN][1000 genomes]
rs633769	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs634741	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs637943	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs640134	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs642248	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs644332	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs644359	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650495	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs651413	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs651897	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs656372	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs658212	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs659902	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs661844	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs663254	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs668766	0.81[EUR][1000 genomes]
rs672391	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs674933	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs675799	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs677875	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs680971	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs683097	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs684996	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs685393	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs685848	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs687708	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs699009	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7367884	0.98[ASN][1000 genomes]
rs7515450	0.98[ASN][1000 genomes]
rs7518152	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs812097	0.84[EUR][1000 genomes]
rs9425188	0.81[AFR][1000 genomes];0.88[ASN][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	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
5	esv1850497	chr1:78596312-78645701	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs633227	NEXN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 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	chr1:78580200-78608600	Weak transcription	HepG2	liver
4	chr1:78584200-78630600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr1:78586400-78608600	Weak transcription	Colonic Mucosa	Colon
6	chr1:78587400-78607200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:78594600-78600000	Weak transcription	Fetal Intestine Small	intestine
8	chr1:78594600-78600400	Weak transcription	Fetal Intestine Large	intestine
9	chr1:78594600-78604600	Weak transcription	Liver	Liver
10	chr1:78598600-78600000	Strong transcription	Duodenum Mucosa	Duodenum

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