Variant report

Variant	rs12757220
Chromosome Location	chr1:225984238-225984239
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225982535..225984252-chr1:225996145..225998557,3	MCF-7	breast:
2	chr1:225976942..225979751-chr1:225984143..225986122,2	K562	blood:
3	chr1:225982192..225984377-chr1:225987070..225988725,2	K562	blood:

Variant related genes	Relation type
ENSG00000143819	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10737418	0.86[EUR][1000 genomes]
rs10737419	0.85[EUR][1000 genomes]
rs10737420	0.85[EUR][1000 genomes]
rs10753409	0.85[EUR][1000 genomes]
rs10799323	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10915876	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10915877	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11581798	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11583520	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11584433	0.80[AFR][1000 genomes]
rs11589896	0.86[AFR][1000 genomes]
rs11808973	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12045518	0.87[AFR][1000 genomes]
rs12047698	0.88[AFR][1000 genomes]
rs12727007	0.85[EUR][1000 genomes]
rs12735768	0.88[AFR][1000 genomes]
rs12741681	0.83[EUR][1000 genomes]
rs12744609	0.82[EUR][1000 genomes]
rs12746838	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12757406	0.83[AFR][1000 genomes]
rs1467143	0.83[EUR][1000 genomes]
rs4653679	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4653684	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4653685	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4653686	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6426089	0.83[EUR][1000 genomes]
rs6687036	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71646745	0.84[AFR][1000 genomes]
rs71646746	0.84[AFR][1000 genomes]
rs7530073	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225973800-225986000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:225974600-225985600	Weak transcription	Fetal Heart	heart
3	chr1:225975000-225997200	Weak transcription	Brain Substantia Nigra	brain
4	chr1:225975000-225997400	Weak transcription	Aorta	Aorta
5	chr1:225976200-225984400	Weak transcription	HepG2	liver
6	chr1:225976200-225989000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr1:225978400-225984400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:225978600-225988200	Weak transcription	NHDF-Ad	bronchial
9	chr1:225978800-225984800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:225978800-225985600	Weak transcription	HMEC	breast
11	chr1:225978800-225989800	Weak transcription	HSMMtube	muscle
12	chr1:225978800-225997200	Weak transcription	K562	blood
13	chr1:225979000-225985800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr1:225979000-225986800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:225979000-225987400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:225979000-225993200	Weak transcription	HUVEC	blood vessel
17	chr1:225979200-225997200	Weak transcription	Right Ventricle	heart
18	chr1:225979600-225985400	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:225979600-225987600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:225979600-225997200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:225979600-225997400	Weak transcription	Lung	lung
22	chr1:225979600-225997800	Weak transcription	Gastric	stomach
23	chr1:225979800-225985000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:225979800-225985000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:225979800-225985200	Weak transcription	Esophagus	oesophagus
26	chr1:225979800-225988400	Weak transcription	Liver	Liver
27	chr1:225979800-225997200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:225979800-225997200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr1:225979800-225997200	Weak transcription	A549	lung
30	chr1:225979800-225997400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:225979800-225997600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:225979800-225997600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:225980000-225984600	Weak transcription	NH-A	brain
34	chr1:225980000-225985600	Weak transcription	Spleen	Spleen
35	chr1:225980000-225987400	Weak transcription	Brain Angular Gyrus	brain
36	chr1:225980000-225988600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:225980000-225990800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:225980000-225997200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:225980000-225997200	Weak transcription	Fetal Stomach	stomach
40	chr1:225980000-225997200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:225980000-225997200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr1:225980000-225997400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:225980000-225997600	Weak transcription	Left Ventricle	heart
44	chr1:225980200-225985200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr1:225980200-225985400	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr1:225981200-225997200	Weak transcription	Adipose Nuclei	Adipose
47	chr1:225982200-225984400	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr1:225982200-225985000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:225982200-225997200	Weak transcription	Thymus	Thymus
50	chr1:225982200-225997400	Weak transcription	Fetal Muscle Leg	muscle

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