Variant report

Variant	rs633769
Chromosome Location	chr1:78607374-78607375
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78605308..78608170-chr1:78609160..78611288,2	MCF-7	breast:

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1407747	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1407748	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1510245	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1625234	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1770307	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4258184	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4285658	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4650607	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs488469	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs494496	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs501774	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs507045	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs513245	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs513977	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs521029	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs522952	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs523751	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs524757	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs526723	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs531841	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs534283	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs540742	0.86[EUR][1000 genomes]
rs554298	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs557688	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs558643	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs561289	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs561300	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs566236	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs577978	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs580426	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs582281	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs582395	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs582795	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs584660	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs585072	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs585100	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs586333	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs587433	0.86[EUR][1000 genomes]
rs591343	0.82[AFR][1000 genomes]
rs593652	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs595384	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs597063	0.82[AFR][1000 genomes]
rs597272	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs599417	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs600781	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs605659	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs609359	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs609390	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs610508	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs612486	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs614836	0.93[AMR][1000 genomes]
rs614963	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs616332	0.86[EUR][1000 genomes]
rs617195	0.84[EUR][1000 genomes]
rs618063	0.82[AFR][1000 genomes]
rs618551	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs618593	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs621524	0.85[EUR][1000 genomes]
rs624766	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs627661	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs629947	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs633227	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs634741	0.82[AFR][1000 genomes]
rs637943	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs642248	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs644332	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs644359	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs650495	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs651413	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs651897	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs656372	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs658212	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs659902	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs661844	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs663254	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs672391	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs674933	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs675799	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs677875	0.82[AFR][1000 genomes]
rs680971	0.82[AFR][1000 genomes]
rs683097	0.82[AFR][1000 genomes]
rs684996	0.82[AFR][1000 genomes]
rs685393	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs685848	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs687708	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs699009	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7367884	0.91[ASN][1000 genomes]
rs7515450	0.91[ASN][1000 genomes]
rs7518152	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs809911	0.81[AMR][1000 genomes]
rs9425188	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][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	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
2	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
3	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
4	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
5	esv3348609	chr1:78607051-78607824	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv3352364	chr1:78607054-78607825	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs633769	NEXN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78555400-78608600	Weak transcription	Pancreas	Pancrea
2	chr1:78580200-78608600	Weak transcription	HepG2	liver
3	chr1:78584200-78630600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr1:78586400-78608600	Weak transcription	Colonic Mucosa	Colon
5	chr1:78603000-78608400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:78603200-78609000	Weak transcription	Fetal Stomach	stomach
7	chr1:78603400-78608400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:78605600-78607400	Enhancers	Liver	Liver
9	chr1:78606200-78608000	Enhancers	Fetal Intestine Small	intestine
10	chr1:78607200-78607400	Enhancers	GM12878-XiMat	blood
11	chr1:78607200-78607800	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr1:78607200-78608000	Enhancers	Duodenum Mucosa	Duodenum
13	chr1:78607200-78609600	Enhancers	Fetal Intestine Large	intestine
14	chr1:78607200-78609600	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr1:78607200-78609800	Enhancers	Small Intestine	intestine

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