Variant report

Variant	rs9304040
Chromosome Location	chr18:9558240-9558241
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	CTCF	chr18:9558220-9558370	SAEC	small airway:	n/a	n/a
2	CTCF	chr18:9558140-9558290	GM12801	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:9556869..9560926-chr18:9561535..9563194,3	K562	blood:
2	chr18:9550795..9553534-chr18:9556478..9558367,2	K562	blood:
3	chr18:9557516..9559867-chr18:9563562..9566089,3	K562	blood:

Variant related genes	Relation type
PPP4R1	TF binding region
ENSG00000154845	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10451359	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11081484	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11874827	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12458145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13381718	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2306134	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28366801	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28838295	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28879133	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2903505	0.82[CEU][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap]
rs328994	0.86[JPT][hapmap]
rs3826562	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3898762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56817979	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57356844	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58359806	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60220573	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7231313	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7233002	0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7239271	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7239728	0.87[CHB][hapmap]
rs745218	0.88[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes]
rs8085047	0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9945701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9946235	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9946612	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9948831	0.89[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes]
rs9949507	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9951382	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9961558	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9965762	0.88[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv833585	chr18:9401630-9597291	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	esv3693417	chr18:9512985-9693638	Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv458024	chr18:9558240-9828448	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv576448	chr18:9558240-9828448	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9304040	RAB31	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9544000-9570200	Strong transcription	Fetal Intestine Large	intestine
2	chr18:9544000-9575600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr18:9544200-9563600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr18:9544600-9561600	Strong transcription	Stomach Smooth Muscle	stomach
5	chr18:9544600-9563600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr18:9544600-9563600	Strong transcription	Brain Cingulate Gyrus	brain
7	chr18:9544600-9564200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr18:9544600-9564200	Strong transcription	Placenta	Placenta
9	chr18:9544800-9562000	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr18:9544800-9564600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr18:9544800-9565000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr18:9544800-9572200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr18:9544800-9572400	Strong transcription	Primary T cells from cord blood	blood
14	chr18:9545000-9562600	Strong transcription	Duodenum Smooth Muscle	Duodenum
15	chr18:9545000-9563800	Strong transcription	Osteobl	bone
16	chr18:9545000-9564200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr18:9545000-9564200	Strong transcription	Adipose Nuclei	Adipose
18	chr18:9545000-9564400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr18:9545200-9560400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr18:9545200-9561400	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr18:9545200-9561600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr18:9545200-9563400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr18:9545200-9572600	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr18:9545400-9560000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr18:9545400-9564000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr18:9545800-9563600	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr18:9545800-9564200	Strong transcription	Fetal Thymus	thymus
28	chr18:9545800-9565000	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr18:9545800-9570200	Strong transcription	Duodenum Mucosa	Duodenum
30	chr18:9545800-9583600	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr18:9545800-9595200	Strong transcription	Dnd41	blood
32	chr18:9546000-9563800	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr18:9546200-9559600	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr18:9546200-9560200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr18:9546200-9564200	Strong transcription	Left Ventricle	heart
36	chr18:9546400-9560200	Strong transcription	Brain Angular Gyrus	brain
37	chr18:9546400-9563600	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr18:9547000-9559600	Strong transcription	K562	blood
39	chr18:9547000-9564000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr18:9547200-9559600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr18:9548800-9558600	Strong transcription	Hela-S3	cervix
42	chr18:9549000-9562600	Strong transcription	Rectal Smooth Muscle	rectum
43	chr18:9549600-9581800	Weak transcription	Psoas Muscle	Psoas
44	chr18:9550200-9559200	Weak transcription	Stomach Mucosa	stomach
45	chr18:9551000-9612200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr18:9552200-9558800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr18:9552200-9565800	Strong transcription	HSMM	muscle
48	chr18:9552200-9565800	Strong transcription	NH-A	brain
49	chr18:9552400-9560800	Strong transcription	Colon Smooth Muscle	Colon
50	chr18:9552400-9564200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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