Variant report

Variant	rs278853
Chromosome Location	chr1:78130243-78130244
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:78128460..78130413-chr1:78144982..78147332,2	K562	blood:
2	chr1:78123471..78126359-chr1:78128834..78131404,3	K562	blood:
3	chr1:78129208..78133797-chr1:78137082..78139912,5	K562	blood:
4	chr1:78129092..78131058-chr1:78135952..78139290,4	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs17100758	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1968027	0.87[ASN][1000 genomes]
rs278846	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28735417	1.00[GIH][hapmap]
rs3736313	0.86[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57075265	0.90[ASN][1000 genomes]
rs61777140	0.84[EUR][1000 genomes]
rs7525870	0.82[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs7535908	0.96[LWK][hapmap]
rs7536433	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs9787306	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.91[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	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv870709	chr1:78016517-78198322	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv3337461	chr1:78036000-78153859	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv830303	chr1:78090824-78308765	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs278853	NEXN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78099000-78147200	Weak transcription	Gastric	stomach
2	chr1:78099200-78132400	Weak transcription	Colon Smooth Muscle	Colon
3	chr1:78100800-78133200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:78105200-78131800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:78107600-78146000	Weak transcription	Fetal Kidney	kidney
6	chr1:78110400-78138000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:78111200-78147200	Weak transcription	Esophagus	oesophagus
8	chr1:78111400-78130800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:78111400-78137400	Weak transcription	HUVEC	blood vessel
10	chr1:78111400-78137600	Weak transcription	Hela-S3	cervix
11	chr1:78112200-78139000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:78114800-78135000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr1:78114800-78135800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:78116800-78144600	Weak transcription	NHEK	skin
15	chr1:78117000-78130600	Weak transcription	Liver	Liver
16	chr1:78117000-78130600	Weak transcription	Brain Angular Gyrus	brain
17	chr1:78117000-78130800	Weak transcription	K562	blood
18	chr1:78117200-78144400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:78117400-78134800	Weak transcription	Osteobl	bone
20	chr1:78117400-78137200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:78117400-78138000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:78117400-78141800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:78117400-78147200	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr1:78117600-78137400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:78117600-78137600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:78117600-78138200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:78117600-78139800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr1:78117600-78146000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:78117600-78147200	Weak transcription	Thymus	Thymus
30	chr1:78118200-78137200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr1:78118600-78130800	Weak transcription	Brain Hippocampus Middle	brain
32	chr1:78118600-78146000	Weak transcription	Primary B cells from peripheral blood	blood
33	chr1:78118800-78130600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr1:78119000-78130600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:78119000-78130600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:78119000-78130800	Weak transcription	NHDF-Ad	bronchial
37	chr1:78119000-78139000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:78119000-78145600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr1:78119000-78146000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:78119200-78130400	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr1:78119400-78131400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:78119400-78147200	Weak transcription	Fetal Muscle Leg	muscle
43	chr1:78120800-78147200	Weak transcription	Lung	lung
44	chr1:78121400-78130800	Weak transcription	Small Intestine	intestine
45	chr1:78121400-78133400	Weak transcription	Primary T cells from cord blood	blood
46	chr1:78121400-78137600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:78121400-78137600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:78121600-78137600	Weak transcription	A549	lung
49	chr1:78121800-78130600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:78123000-78131400	Weak transcription	Primary T cells fromperipheralblood	blood

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