Variant report

Variant	rs62549130
Chromosome Location	chr9:18825103-18825104
allele	C/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	RAD21	chr9:18824937-18825175	IMR90	lung:	n/a	n/a
2	CTCF	chr9:18825040-18825190	AG04449	skin:	n/a	n/a
3	CTCF	chr9:18825100-18825250	HVMF	connective:	n/a	n/a
4	CTCF	chr9:18825100-18825250	AoAF	blood vessel:	n/a	n/a
5	CTCF	chr9:18825080-18825230	HPF	lung:	n/a	n/a
6	CTCF	chr9:18825060-18825210	HCFaa	heart:	n/a	n/a
7	EBF1	chr9:18825014-18825239	GM12878	blood:	n/a	chr9:18825101-18825112 chr9:18825101-18825111
8	CTCF	chr9:18825020-18825170	HMF	breast:	n/a	n/a
9	CTCF	chr9:18825100-18825350	AG04450	lung:	n/a	n/a
10	CTCF	chr9:18825080-18825230	AG04450	lung:	n/a	n/a
11	CTCF	chr9:18825100-18825250	HPF	lung:	n/a	n/a
12	CTCF	chr9:18825080-18825230	HCPEpiC	choroid plexus:	n/a	n/a
13	KAP1	chr9:18825029-18825459	HEK293	kidney:	n/a	n/a
14	CTCF	chr9:18825080-18825230	NHDF-neo	bronchial:	n/a	n/a
15	CTCF	chr9:18825080-18825230	HMEC	breast:	n/a	n/a
16	CTCF	chr9:18825100-18825250	HBMEC	blood vessel:	n/a	n/a
17	CTCF	chr9:18825060-18825210	HCPEpiC	choroid plexus:	n/a	n/a
18	CTCF	chr9:18825100-18825250	HEK293	kidney:	n/a	n/a

Variant related genes	Relation type
ADAMTSL1	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10811046	0.81[ASN][1000 genomes]
rs11795248	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11999522	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16937127	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4313669	1.00[ASN][1000 genomes]
rs4497057	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55921006	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56160805	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56325857	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58686714	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59852857	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62549134	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62549135	0.91[ASN][1000 genomes]
rs62549136	0.82[ASN][1000 genomes]
rs7852764	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7871789	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9695755	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9696796	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9696918	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491807	chr9:18243672-19009770	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv525659	chr9:18288212-19009041	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1019127	chr9:18288271-18996288	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1029449	chr9:18414752-18829127	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv540077	chr9:18414752-18829127	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv1030931	chr9:18414752-18903530	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv892692	chr9:18519699-19045502	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv949111	chr9:18758205-18994588	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18788000-18825200	Weak transcription	HUVEC	blood vessel
2	chr9:18806400-18826000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:18815400-18829200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr9:18818000-18845200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:18818200-18828800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr9:18821600-18825400	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr9:18822000-18826800	Enhancers	Fetal Heart	heart
8	chr9:18822200-18825200	Weak transcription	NH-A	brain
9	chr9:18822600-18826000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr9:18822800-18826000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr9:18823000-18825400	Enhancers	Stomach Mucosa	stomach
12	chr9:18823000-18826400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr9:18823000-18834400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr9:18823400-18826600	Enhancers	Lung	lung
15	chr9:18823600-18825200	Enhancers	Pancreas	Pancrea
16	chr9:18824000-18825200	Enhancers	Gastric	stomach
17	chr9:18824000-18826200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr9:18824000-18827400	Enhancers	Primary T cells from cord blood	blood
19	chr9:18824000-18827800	Enhancers	Fetal Thymus	thymus
20	chr9:18824200-18825200	Enhancers	Osteobl	bone
21	chr9:18824200-18825400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr9:18824200-18825400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr9:18824200-18825400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr9:18824200-18825400	Enhancers	Colon Smooth Muscle	Colon
25	chr9:18824200-18825600	Genic enhancers	NHDF-Ad	bronchial
26	chr9:18824200-18825800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr9:18824400-18825200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr9:18824400-18825400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr9:18824400-18825400	Genic enhancers	Muscle Satellite Cultured Cells	--
30	chr9:18824400-18825400	Enhancers	Aorta	Aorta
31	chr9:18824400-18825400	Enhancers	Liver	Liver
32	chr9:18824400-18825400	Enhancers	Right Atrium	heart
33	chr9:18824400-18825400	Enhancers	Right Ventricle	heart
34	chr9:18824400-18825400	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr9:18824400-18825400	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr9:18824400-18825400	Genic enhancers	HSMM	muscle
37	chr9:18824400-18825800	Enhancers	Adipose Nuclei	Adipose
38	chr9:18824400-18826600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr9:18824800-18825800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr9:18825000-18825200	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr9:18825000-18825400	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr9:18825000-18825400	Enhancers	Esophagus	oesophagus
43	chr9:18825000-18825400	Enhancers	Ovary	ovary
44	chr9:18825000-18825400	Enhancers	Psoas Muscle	Psoas
45	chr9:18825000-18825400	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr9:18825000-18825400	Enhancers	Stomach Smooth Muscle	stomach
47	chr9:18825000-18825400	Enhancers	HepG2	liver
48	chr9:18825000-18825400	Enhancers	HSMMtube	muscle
49	chr9:18825000-18825600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr9:18825000-18825600	Enhancers	Dnd41	blood

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