Variant report

Variant	rs2253778
Chromosome Location	chr9:72027854-72027855
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71650287..71651089-chr9:72027660..72028217,2	K562	blood:
2	chr9:71939359..71941808-chr9:72025736..72028094,2	MCF-7	breast:
3	chr9:72027288..72028201-chr9:72161004..72161637,2	MCF-7	breast:
4	chr9:72027335..72027966-chr9:72164135..72164934,2	MCF-7	breast:
5	chr9:71907137..71907714-chr9:72027328..72028069,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165060	Chromatin interaction
ENSG00000135063	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10511966	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs10867682	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs11138902	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs11139065	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs11139224	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs11139245	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs11139246	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs11139289	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1236984	0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12378157	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs12378318	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs12551899	0.82[JPT][hapmap]
rs12553491	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs13286303	0.91[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes]
rs13286400	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs13290847	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs13290881	0.82[JPT][hapmap]
rs13291679	0.85[JPT][hapmap]
rs13296504	0.91[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs13297121	0.86[JPT][hapmap]
rs1475641	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs17412941	0.82[JPT][hapmap];0.88[YRI][hapmap]
rs1757961	0.85[ASN][1000 genomes]
rs1761284	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1855529	0.82[JPT][hapmap];0.80[YRI][hapmap]
rs2297420	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2777860	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2777864	0.81[AMR][1000 genomes]
rs3897757	0.81[ASN][1000 genomes]
rs4307408	0.87[JPT][hapmap]
rs4351475	0.86[JPT][hapmap];0.88[YRI][hapmap]
rs4744884	0.86[JPT][hapmap];0.88[YRI][hapmap]
rs4744885	0.82[JPT][hapmap]
rs4744893	0.91[JPT][hapmap];0.89[YRI][hapmap]
rs4744898	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4744899	0.81[ASN][1000 genomes]
rs7028920	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs7853058	0.82[JPT][hapmap]
rs867365	0.91[JPT][hapmap];0.88[YRI][hapmap]
rs867366	0.91[JPT][hapmap]
rs9410534	0.90[ASN][1000 genomes]
rs9410823	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv893429	chr9:71961923-72047337	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv893430	chr9:71968730-72036369	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1047593	chr9:71971536-72180583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS 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	8 gene(s)	inside rSNPs	diseases
5	nsv1035633	chr9:71995963-72176984	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv893431	chr9:72003036-72048098	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv8522	chr9:72009272-72034735	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv2757340	chr9:72018246-72048098	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv2759694	chr9:72018246-72048098	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72026800-72028000	Enhancers	iPS-20b Cell Line	embryonic stem cell
2	chr9:72026800-72028400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:72027000-72028000	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr9:72027000-72028000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:72027000-72028000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr9:72027000-72028200	Enhancers	H1 Cell Line	embryonic stem cell
7	chr9:72027000-72028400	Enhancers	Esophagus	oesophagus
8	chr9:72027000-72040000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:72027200-72028000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr9:72027200-72028000	Enhancers	Fetal Heart	heart
11	chr9:72027200-72028000	Enhancers	Right Ventricle	heart
12	chr9:72027400-72028000	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr9:72027400-72028000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr9:72027400-72028000	Enhancers	Brain Hippocampus Middle	brain
15	chr9:72027400-72028200	Enhancers	Fetal Lung	lung
16	chr9:72027600-72028000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:72027600-72028000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr9:72027600-72028000	Active TSS	Brain Germinal Matrix	brain
19	chr9:72027600-72028000	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr9:72027600-72028000	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr9:72027600-72028000	Active TSS	Fetal Brain Female	brain
22	chr9:72027600-72028000	Enhancers	Fetal Muscle Leg	muscle
23	chr9:72027600-72028000	Enhancers	Rectal Smooth Muscle	rectum
24	chr9:72027600-72028000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr9:72027600-72028200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr9:72027600-72028200	Active TSS	Adipose Nuclei	Adipose
27	chr9:72027600-72028200	Enhancers	Ovary	ovary
28	chr9:72027800-72028000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr9:72027800-72028000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr9:72027800-72028000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr9:72027800-72028000	Enhancers	Brain Substantia Nigra	brain
32	chr9:72027800-72028000	Enhancers	Colonic Mucosa	Colon
33	chr9:72027800-72028000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
34	chr9:72027800-72028000	Enhancers	Left Ventricle	heart
35	chr9:72027800-72028000	Flanking Bivalent TSS/Enh	Lung	lung
36	chr9:72027800-72028000	Enhancers	Pancreas	Pancrea
37	chr9:72027800-72028000	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr9:72027800-72028000	Enhancers	Right Atrium	heart
39	chr9:72027800-72028000	Flanking Active TSS	HepG2	liver
40	chr9:72027800-72028000	Flanking Active TSS	HSMM	muscle
41	chr9:72027800-72028000	Enhancers	NH-A	brain
42	chr9:72027800-72028000	Enhancers	NHDF-Ad	bronchial
43	chr9:72027800-72028000	Flanking Active TSS	NHEK	skin
44	chr9:72027800-72028000	Flanking Active TSS	Osteobl	bone
45	chr9:72027800-72028200	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr9:72027800-72028200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr9:72027800-72028200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr9:72027800-72028200	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr9:72027800-72028200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr9:72027800-72028200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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