Variant report

Variant	rs9787306
Chromosome Location	chr1:78070458-78070459
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78070290..78072373-chr1:78147292..78150145,3	K562	blood:
2	chr1:78065469..78069224-chr1:78069679..78073239,3	K562	blood:

Variant related genes	Relation type
ENSG00000036549	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs17100758	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs17385707	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs1968027	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs278839	1.00[MKK][hapmap]
rs278846	0.84[ASN][1000 genomes]
rs278853	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.91[ASN][1000 genomes]
rs3736313	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.89[ASN][1000 genomes]
rs4121165	0.82[EUR][1000 genomes]
rs57075265	0.81[ASN][1000 genomes]
rs7525870	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs7536433	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9787306	DNAJB4	cis	parietal	SCAN
rs9787306	NEXN	cis	multi-tissue	Pritchard
rs9787306	NEXN	cis	lymphoblastoid	seeQTL
rs9787306	NEXN	Cis_1M	lymphoblastoid	RTeQTL
rs9787306	DNAJB4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78024800-78071000	Weak transcription	Gastric	stomach
2	chr1:78032600-78070800	Weak transcription	Aorta	Aorta
3	chr1:78032800-78070600	Weak transcription	Small Intestine	intestine
4	chr1:78033200-78072600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:78033600-78070800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:78038600-78071000	Weak transcription	Pancreas	Pancrea
7	chr1:78039000-78070800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:78042000-78070800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:78042000-78074600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:78042200-78073800	Weak transcription	Fetal Brain Female	brain
11	chr1:78047000-78070800	Weak transcription	Lung	lung
12	chr1:78047000-78071200	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr1:78047600-78070800	Weak transcription	HSMMtube	muscle
14	chr1:78047600-78071000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr1:78047600-78071600	Weak transcription	Thymus	Thymus
16	chr1:78047600-78072400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:78047600-78072600	Weak transcription	Fetal Kidney	kidney
18	chr1:78047600-78074600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr1:78047600-78074800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:78047600-78085600	Weak transcription	NHLF	lung
21	chr1:78047800-78070800	Weak transcription	Left Ventricle	heart
22	chr1:78047800-78070800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:78047800-78071000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr1:78047800-78074200	Weak transcription	Hela-S3	cervix
25	chr1:78047800-78074800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:78047800-78086200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:78047800-78090000	Weak transcription	NH-A	brain
28	chr1:78048000-78074600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:78048000-78077800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr1:78048000-78097400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:78048200-78070600	Weak transcription	HMEC	breast
32	chr1:78048600-78070800	Weak transcription	Fetal Stomach	stomach
33	chr1:78048800-78070800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:78048800-78071000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:78048800-78071000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:78049000-78072400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr1:78050000-78075000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:78053600-78070800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:78054000-78074800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr1:78055400-78070800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:78056600-78074000	Weak transcription	Colon Smooth Muscle	Colon
42	chr1:78057000-78070600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr1:78057200-78070800	Weak transcription	Spleen	Spleen
44	chr1:78058000-78074800	Weak transcription	Brain Germinal Matrix	brain
45	chr1:78058200-78070800	Weak transcription	Psoas Muscle	Psoas
46	chr1:78059000-78083200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr1:78061000-78070800	Weak transcription	HUVEC	blood vessel
48	chr1:78061200-78070800	Weak transcription	NHEK	skin
49	chr1:78061200-78072400	Weak transcription	GM12878-XiMat	blood
50	chr1:78062800-78074200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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