Variant report

Variant	rs12470253
Chromosome Location	chr2:55821672-55821673
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55818907..55824295-chr2:55841098..55846037,6	MCF-7	breast:
2	chr2:55820891..55824510-chr2:55834569..55837738,3	K562	blood:

Variant related genes	Relation type
ENSG00000138041	Chromatin interaction
ENSG00000272606	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10496043	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10496047	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12471135	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12472098	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12476169	1.00[ASN][1000 genomes]
rs1579780	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17278148	1.00[ASN][1000 genomes]
rs17278197	1.00[ASN][1000 genomes]
rs17369240	1.00[ASN][1000 genomes]
rs17737937	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17792798	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17792822	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17800851	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs41281507	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4671247	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4671251	1.00[ASN][1000 genomes]
rs4671256	1.00[ASN][1000 genomes]
rs4672053	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4672057	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4672059	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4672060	1.00[ASN][1000 genomes]
rs4672062	1.00[ASN][1000 genomes]
rs4672064	1.00[ASN][1000 genomes]
rs55635545	1.00[ASN][1000 genomes]
rs55919620	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56071955	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56227318	0.84[EUR][1000 genomes]
rs56286204	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56299972	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56769899	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6729021	1.00[ASN][1000 genomes]
rs6741902	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72812189	1.00[ASN][1000 genomes]
rs72812199	1.00[ASN][1000 genomes]
rs72814203	1.00[ASN][1000 genomes]
rs72814204	1.00[ASN][1000 genomes]
rs72814206	1.00[ASN][1000 genomes]
rs72814216	1.00[ASN][1000 genomes]
rs72814217	1.00[ASN][1000 genomes]
rs72814219	1.00[ASN][1000 genomes]
rs72814230	1.00[ASN][1000 genomes]
rs72814233	1.00[ASN][1000 genomes]
rs72814235	1.00[ASN][1000 genomes]
rs72814236	1.00[ASN][1000 genomes]
rs72814242	1.00[ASN][1000 genomes]
rs73940304	1.00[ASN][1000 genomes]
rs7568378	1.00[ASN][1000 genomes]
rs7569732	1.00[ASN][1000 genomes]
rs7584017	1.00[ASN][1000 genomes]
rs7586423	1.00[ASN][1000 genomes]
rs7603050	1.00[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	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv874160	chr2:55713102-55828974	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv525434	chr2:55716650-55841640	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55752600-55831400	Weak transcription	Stomach Mucosa	stomach
2	chr2:55779600-55831400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr2:55788800-55825200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:55789800-55822800	Weak transcription	HSMMtube	muscle
5	chr2:55789800-55843600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:55790200-55829000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:55790200-55842400	Weak transcription	Fetal Brain Male	brain
8	chr2:55790400-55836200	Weak transcription	Fetal Heart	heart
9	chr2:55794400-55825200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:55794400-55829000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:55796800-55823800	Weak transcription	Thymus	Thymus
12	chr2:55796800-55825200	Weak transcription	Brain Substantia Nigra	brain
13	chr2:55796800-55825600	Weak transcription	Pancreas	Pancrea
14	chr2:55796800-55829400	Weak transcription	Esophagus	oesophagus
15	chr2:55796800-55842600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:55797000-55824200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:55797000-55828000	Weak transcription	Aorta	Aorta
18	chr2:55797000-55829400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:55797000-55829600	Weak transcription	Gastric	stomach
20	chr2:55803000-55838800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr2:55803200-55823800	Weak transcription	Lung	lung
22	chr2:55804000-55824000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:55804400-55825200	Weak transcription	K562	blood
24	chr2:55806600-55825600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:55806800-55825200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr2:55807400-55823000	Weak transcription	Fetal Kidney	kidney
27	chr2:55808200-55824800	Weak transcription	Colonic Mucosa	Colon
28	chr2:55810600-55829600	Weak transcription	Brain Hippocampus Middle	brain
29	chr2:55811400-55829400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr2:55811600-55825000	Weak transcription	Fetal Brain Female	brain
31	chr2:55812400-55823400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr2:55812600-55823000	Weak transcription	Fetal Lung	lung
33	chr2:55814200-55822400	Weak transcription	Primary B cells from cord blood	blood
34	chr2:55814200-55825200	Weak transcription	HUVEC	blood vessel
35	chr2:55814200-55825600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr2:55814200-55829000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr2:55814200-55829400	Weak transcription	Brain Germinal Matrix	brain
38	chr2:55814400-55824200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr2:55814400-55826000	Weak transcription	GM12878-XiMat	blood
40	chr2:55815000-55823200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr2:55815200-55825400	Weak transcription	Hela-S3	cervix
42	chr2:55815400-55823800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:55815600-55822400	Weak transcription	Fetal Stomach	stomach
44	chr2:55815800-55822200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr2:55815800-55822800	Weak transcription	Liver	Liver
46	chr2:55815800-55822800	Weak transcription	Fetal Muscle Leg	muscle
47	chr2:55815800-55823000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr2:55816000-55823200	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr2:55816000-55823400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr2:55816000-55824800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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