Variant report

Variant	rs518636
Chromosome Location	chr9:116363146-116363147
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116353752..116357757-chr9:116360190..116364418,7	K562	blood:
2	chr9:116354705..116357000-chr9:116361323..116363210,2	MCF-7	breast:
3	chr9:116348874..116350912-chr9:116362853..116364416,2	MCF-7	breast:
4	chr9:116357889..116361731-chr9:116362609..116366505,5	MCF-7	breast:
5	chr9:116343200..116345201-chr9:116363106..116364913,2	MCF-7	breast:
6	chr9:116362421..116364215-chr9:116382528..116385259,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138835	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1051013	0.84[EUR][1000 genomes]
rs10739393	0.85[JPT][hapmap]
rs12350531	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12685417	0.88[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap]
rs12686023	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs17187621	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4979253	0.92[JPT][hapmap]
rs4979261	0.85[JPT][hapmap]
rs567743	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs568557	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72763856	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs818714	0.85[JPT][hapmap]
rs944343	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv893747	chr9:116214058-116386438	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS 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	13 gene(s)	inside rSNPs	diseases
3	nsv526579	chr9:116244982-116391162	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv893748	chr9:116308709-116421786	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
6	nsv466509	chr9:116356516-116396098	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv615216	chr9:116356516-116396098	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs518636	ATP6V1G1	cis	parietal	SCAN
rs518636	C9orf91	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116352400-116363200	Weak transcription	Thymus	Thymus
2	chr9:116357400-116364800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr9:116357400-116364800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr9:116357800-116364400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr9:116358000-116371800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr9:116358400-116363400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr9:116359200-116363400	Enhancers	Psoas Muscle	Psoas
8	chr9:116359600-116363800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:116359800-116364400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:116360000-116364000	Genic enhancers	NHLF	lung
11	chr9:116360000-116364200	Weak transcription	Fetal Thymus	thymus
12	chr9:116360200-116363600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr9:116360200-116363600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr9:116360200-116363800	Enhancers	Right Atrium	heart
15	chr9:116360200-116364000	Weak transcription	GM12878-XiMat	blood
16	chr9:116360200-116365400	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr9:116360200-116366400	Enhancers	Placenta	Placenta
18	chr9:116360400-116363400	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr9:116360400-116363600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr9:116360400-116363600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr9:116360400-116364000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr9:116360400-116364200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr9:116360400-116364400	Weak transcription	Small Intestine	intestine
24	chr9:116360400-116364600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr9:116360400-116364600	Weak transcription	Fetal Brain Female	brain
26	chr9:116360400-116371800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr9:116360600-116363200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr9:116360600-116363400	Weak transcription	Brain Hippocampus Middle	brain
29	chr9:116360600-116363600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr9:116360600-116363800	Weak transcription	Brain Angular Gyrus	brain
31	chr9:116360600-116363800	Weak transcription	Esophagus	oesophagus
32	chr9:116360600-116364000	Weak transcription	Primary B cells from peripheral blood	blood
33	chr9:116360600-116364000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr9:116360600-116364000	Weak transcription	Stomach Mucosa	stomach
35	chr9:116360600-116364200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr9:116360600-116365800	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr9:116360600-116366000	Enhancers	Right Ventricle	heart
38	chr9:116360800-116364200	Weak transcription	Gastric	stomach
39	chr9:116360800-116364400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr9:116360800-116366000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr9:116360800-116366000	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr9:116360800-116366000	Enhancers	NHDF-Ad	bronchial
43	chr9:116360800-116366600	Enhancers	Liver	Liver
44	chr9:116361000-116363200	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr9:116361000-116364000	Weak transcription	Colonic Mucosa	Colon
46	chr9:116361000-116364000	Weak transcription	Colon Smooth Muscle	Colon
47	chr9:116361000-116364400	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr9:116361000-116364400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr9:116361000-116364400	Weak transcription	Duodenum Mucosa	Duodenum
50	chr9:116361000-116364600	Weak transcription	Brain Germinal Matrix	brain

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