Variant report

Variant	rs278839
Chromosome Location	chr1:78107874-78107875
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:78107861-78107962	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
RN7SL370P	TF binding region

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs17380592	1.00[ASW][hapmap];1.00[CHD][hapmap]
rs9787306	1.00[MKK][hapmap]

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
rs278839	NEXN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78076400-78113000	Weak transcription	Psoas Muscle	Psoas
2	chr1:78094800-78113600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:78096200-78110400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:78096200-78111000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:78098400-78113400	Weak transcription	Pancreas	Pancrea
6	chr1:78098400-78116800	Weak transcription	Right Ventricle	heart
7	chr1:78098600-78110600	Weak transcription	Lung	lung
8	chr1:78098600-78111400	Weak transcription	Brain Germinal Matrix	brain
9	chr1:78098600-78113200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:78098800-78108000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:78098800-78110200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr1:78098800-78110600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr1:78099000-78108000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:78099000-78108200	Weak transcription	Colonic Mucosa	Colon
15	chr1:78099000-78110200	Weak transcription	Placenta	Placenta
16	chr1:78099000-78110600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:78099000-78110600	Weak transcription	Esophagus	oesophagus
18	chr1:78099000-78110600	Weak transcription	Ovary	ovary
19	chr1:78099000-78110600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:78099000-78110600	Weak transcription	Thymus	Thymus
21	chr1:78099000-78111600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:78099000-78112600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:78099000-78113800	Weak transcription	Fetal Brain Male	brain
24	chr1:78099000-78113800	Weak transcription	Spleen	Spleen
25	chr1:78099000-78147200	Weak transcription	Gastric	stomach
26	chr1:78099200-78110400	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr1:78099200-78110400	Weak transcription	Fetal Brain Female	brain
28	chr1:78099200-78110600	Weak transcription	Left Ventricle	heart
29	chr1:78099200-78110600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr1:78099200-78114000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr1:78099200-78115000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:78099200-78120800	Weak transcription	Small Intestine	intestine
33	chr1:78099200-78132400	Weak transcription	Colon Smooth Muscle	Colon
34	chr1:78099600-78108800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:78099600-78110400	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr1:78099600-78116800	Weak transcription	Aorta	Aorta
37	chr1:78100400-78110600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr1:78100600-78110600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:78100600-78111600	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr1:78100800-78110200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr1:78100800-78110400	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:78100800-78110400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr1:78100800-78115800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr1:78100800-78116600	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr1:78100800-78133200	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr1:78101000-78110600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:78101000-78111000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr1:78101000-78113200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr1:78101400-78110400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr1:78102600-78114400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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