Variant report

Variant	rs503596
Chromosome Location	chr9:136810524-136810525
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:136809714..136811790-chr9:136818542..136820175,2	MCF-7	breast:
2	chr9:136810315..136812430-chr9:136853875..136857440,3	MCF-7	breast:
3	chr9:136810410..136813300-chr9:136824316..136826699,2	MCF-7	breast:
4	chr9:136810475..136813039-chr9:136813457..136816106,3	K562	blood:
5	chr9:136809945..136812192-chr9:136855956..136857665,2	MCF-7	breast:
6	chr9:136809153..136811030-chr9:136812692..136814573,2	MCF-7	breast:
7	chr9:136799983..136801681-chr9:136809502..136811827,2	MCF-7	breast:
8	chr9:136747124..136749714-chr9:136809806..136812182,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160293	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1633757	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1768685	0.88[EUR][1000 genomes]
rs4744527	0.85[EUR][1000 genomes]
rs481964	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs485458	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs532646	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs557327	0.92[CEU][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs561257	0.88[EUR][1000 genomes]
rs562000	0.88[EUR][1000 genomes]
rs578151	0.86[EUR][1000 genomes]
rs619173	0.89[CEU][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs621569	0.89[CEU][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs622543	0.87[EUR][1000 genomes]
rs636541	0.86[EUR][1000 genomes]
rs687644	0.88[EUR][1000 genomes]
rs688091	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs739449	0.89[CEU][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894123	chr9:136682408-136852501	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv894124	chr9:136716399-136870787	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv894125	chr9:136723520-136931957	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv894127	chr9:136747832-136811772	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv894128	chr9:136753246-136906752	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1046310	chr9:136762829-136872226	Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv894130	chr9:136767346-136906752	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv831748	chr9:136788484-136944326	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
9	nsv894131	chr9:136792765-136906752	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv466626	chr9:136807770-136835343	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv615742	chr9:136807770-136835343	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv831749	chr9:136809200-136915764	Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs503596	AGPAT2	cis	cerebellum	SCAN
rs503596	C9orf98	cis	cerebellum	SCAN
rs503596	UBAC1	cis	parietal	SCAN
rs503596	C9orf163	cis	cerebellum	SCAN
rs503596	FCN1	cis	cerebellum	SCAN
rs503596	GFI1B	cis	cerebellum	SCAN
rs503596	PNMA1	trans	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136753000-136813200	Weak transcription	Aorta	Aorta
2	chr9:136784000-136819800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr9:136797800-136811000	Weak transcription	A549	lung
4	chr9:136801000-136815400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr9:136801200-136815600	Weak transcription	Right Atrium	heart
6	chr9:136801200-136815800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr9:136801200-136820200	Weak transcription	Left Ventricle	heart
8	chr9:136801400-136821200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr9:136802000-136815800	Weak transcription	Colonic Mucosa	Colon
10	chr9:136802200-136815800	Strong transcription	Fetal Intestine Small	intestine
11	chr9:136802800-136816200	Weak transcription	Fetal Kidney	kidney
12	chr9:136803000-136813000	Weak transcription	Fetal Lung	lung
13	chr9:136803000-136815200	Weak transcription	HSMMtube	muscle
14	chr9:136803200-136811200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr9:136803200-136821200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr9:136803400-136811000	Weak transcription	Hela-S3	cervix
17	chr9:136803600-136821000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr9:136804200-136813400	Weak transcription	Gastric	stomach
19	chr9:136804200-136815400	Weak transcription	Ovary	ovary
20	chr9:136804200-136815400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr9:136804200-136819800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr9:136804200-136820200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr9:136804200-136821000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr9:136804200-136821200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr9:136804400-136810800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr9:136804400-136814800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr9:136804400-136815000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr9:136805000-136810600	Weak transcription	Lung	lung
29	chr9:136805200-136811000	Weak transcription	HepG2	liver
30	chr9:136805600-136811200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr9:136805800-136811000	Weak transcription	Right Ventricle	heart
32	chr9:136805800-136819400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr9:136806200-136813000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr9:136807400-136813400	Strong transcription	Fetal Stomach	stomach
35	chr9:136807600-136813400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr9:136807800-136810600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr9:136808000-136811200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr9:136808000-136811200	Enhancers	Pancreas	Pancrea
39	chr9:136808400-136811800	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr9:136808400-136815600	Weak transcription	Brain Angular Gyrus	brain
41	chr9:136808600-136810800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr9:136808600-136811400	Enhancers	NH-A	brain
43	chr9:136808600-136813400	Enhancers	Primary B cells from peripheral blood	blood
44	chr9:136808800-136811400	Enhancers	HMEC	breast
45	chr9:136808800-136813600	Enhancers	Primary B cells from cord blood	blood
46	chr9:136809000-136811800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr9:136809000-136812200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr9:136809200-136811200	Enhancers	Muscle Satellite Cultured Cells	--
49	chr9:136809200-136814200	Enhancers	HUVEC	blood vessel
50	chr9:136809400-136810600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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