Variant report

Variant	rs16803
Chromosome Location	chr9:136815357-136815358
allele	C/T
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	chr9:136815263..136820961-chr9:136821414..136825553,6	MCF-7	breast:
2	chr9:136813249..136815512-chr9:136856138..136859094,3	MCF-7	breast:
3	chr9:136814134..136815760-chr9:136832244..136834207,2	MCF-7	breast:
4	chr9:136813341..136815906-chr9:136834550..136837034,2	MCF-7	breast:
5	chr9:136810475..136813039-chr9:136813457..136816106,3	K562	blood:
6	chr9:136813385..136817177-chr9:136818574..136821004,3	MCF-7	breast:
7	chr9:136813894..136816969-chr9:136817141..136821146,4	MCF-7	breast:
8	chr9:136815020..136816601-chr9:136860068..136862429,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160293	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1633759	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16767	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16819	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2256875	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2256876	0.86[EUR][1000 genomes]
rs2810536	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs503376	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs520308	1.00[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.96[ASN][1000 genomes]
rs557500	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs636667	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs637521	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs654182	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs664026	0.93[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs681492	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs681508	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs682388	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs682418	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs694505	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	nsv894132	chr9:136813341-136950691	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16803	SDCCAG3	cis	cerebellum	SCAN
rs16803	GPSM1	cis	parietal	SCAN
rs16803	CELP	cis	parietal	SCAN
rs16803	TOR1B	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136784000-136819800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr9:136801000-136815400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr9:136801200-136815600	Weak transcription	Right Atrium	heart
4	chr9:136801200-136815800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr9:136801200-136820200	Weak transcription	Left Ventricle	heart
6	chr9:136801400-136821200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr9:136802000-136815800	Weak transcription	Colonic Mucosa	Colon
8	chr9:136802200-136815800	Strong transcription	Fetal Intestine Small	intestine
9	chr9:136802800-136816200	Weak transcription	Fetal Kidney	kidney
10	chr9:136803200-136821200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr9:136803600-136821000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr9:136804200-136815400	Weak transcription	Ovary	ovary
13	chr9:136804200-136815400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr9:136804200-136819800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr9:136804200-136820200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr9:136804200-136821000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr9:136804200-136821200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr9:136805800-136819400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr9:136808400-136815600	Weak transcription	Brain Angular Gyrus	brain
20	chr9:136809600-136821000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr9:136810000-136815400	Weak transcription	NHLF	lung
22	chr9:136810400-136815600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr9:136810400-136821200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:136810600-136815400	Weak transcription	HSMM	muscle
25	chr9:136810600-136815600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr9:136810600-136821200	Weak transcription	Osteobl	bone
27	chr9:136810800-136817400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr9:136810800-136818800	Weak transcription	Esophagus	oesophagus
29	chr9:136811200-136815800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr9:136811400-136820200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr9:136811400-136821000	Weak transcription	HMEC	breast
32	chr9:136811600-136819800	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr9:136811800-136815400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr9:136811800-136816400	Weak transcription	Right Ventricle	heart
35	chr9:136811800-136818200	Weak transcription	Fetal Intestine Large	intestine
36	chr9:136811800-136821600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr9:136812200-136817800	Weak transcription	NHEK	skin
38	chr9:136812200-136821800	Weak transcription	Hela-S3	cervix
39	chr9:136812400-136816000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr9:136813000-136817000	Enhancers	Fetal Lung	lung
41	chr9:136813200-136817000	Strong transcription	HepG2	liver
42	chr9:136813400-136815400	Enhancers	H1 Cell Line	embryonic stem cell
43	chr9:136813400-136816800	Enhancers	Fetal Brain Male	brain
44	chr9:136813400-136817000	Enhancers	Spleen	Spleen
45	chr9:136813400-136817200	Enhancers	Fetal Muscle Leg	muscle
46	chr9:136813800-136819000	Weak transcription	Fetal Thymus	thymus
47	chr9:136813800-136819400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr9:136813800-136821000	Weak transcription	Gastric	stomach
49	chr9:136814000-136819000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr9:136814200-136815400	Weak transcription	Lung	lung

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