Variant report

Variant	rs654185
Chromosome Location	chr1:78526657-78526658
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:78518422..78519997-chr1:78524033..78526694,2	K562	blood:
2	chr1:78468253..78471676-chr1:78525525..78529998,6	K562	blood:
3	chr1:78520206..78525011-chr1:78526646..78528908,4	K562	blood:
4	chr1:78484921..78487843-chr1:78526305..78528033,2	K562	blood:
5	chr1:78469696..78471554-chr1:78524530..78528737,5	K562	blood:

Variant related genes	Relation type
ENSG00000162616	Chromatin interaction
ENSG00000273338	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11162412	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12067638	0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3790592	0.94[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs481199	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs483760	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs485005	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5001390	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs501935	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs505301	0.94[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs515662	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs539228	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs565164	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs571255	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs571988	0.94[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs586680	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs587143	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs594852	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs598988	0.80[EUR][1000 genomes]
rs600742	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs610501	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs611820	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs630245	0.94[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs630640	0.95[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs631045	0.94[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap]
rs638668	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs639677	0.95[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs640935	0.90[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs643512	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs657954	0.94[CEU][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs658780	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs664448	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6669039	0.81[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs666995	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6688346	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs677640	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs686716	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7539956	0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs812097	0.88[YRI][hapmap];0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs654185	NEXN	Cis_1M	lymphoblastoid	RTeQTL
rs654185	DNAJB4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78515400-78534200	Weak transcription	HepG2	liver
2	chr1:78519000-78536000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:78519200-78527000	Weak transcription	Fetal Muscle Leg	muscle
4	chr1:78519800-78526800	Weak transcription	Psoas Muscle	Psoas
5	chr1:78520800-78526800	Weak transcription	HSMMtube	muscle
6	chr1:78521600-78526800	Weak transcription	Fetal Intestine Large	intestine
7	chr1:78521600-78526800	Weak transcription	Right Atrium	heart
8	chr1:78521600-78526800	Weak transcription	HMEC	breast
9	chr1:78521600-78534600	Weak transcription	Colonic Mucosa	Colon
10	chr1:78521800-78526800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:78521800-78526800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr1:78521800-78526800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr1:78521800-78527600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:78521800-78527800	Weak transcription	HUVEC	blood vessel
15	chr1:78521800-78534600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:78522000-78527000	Weak transcription	Left Ventricle	heart
17	chr1:78522200-78529800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:78525000-78526800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:78525000-78527000	Weak transcription	NH-A	brain
20	chr1:78525200-78526800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:78525400-78526800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr1:78525400-78534400	Weak transcription	Pancreas	Pancrea
23	chr1:78525600-78534000	Weak transcription	Fetal Intestine Small	intestine
24	chr1:78526200-78527400	Weak transcription	Gastric	stomach
25	chr1:78526600-78528200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:78526600-78528200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:78526600-78528200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:78526600-78528200	Enhancers	HSMM	muscle
29	chr1:78526600-78528200	Enhancers	NHEK	skin
30	chr1:78526600-78528400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:78526600-78528400	Enhancers	Osteobl	bone

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