Variant report

Variant	rs12205420
Chromosome Location	chr6:15294645-15294646
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:15287044..15289498-chr6:15293703..15295568,2	K562	blood:
2	chr6:15288769..15290652-chr6:15292771..15295719,2	MCF-7	breast:
3	chr6:15294357..15295870-chr6:15319327..15321466,2	K562	blood:
4	chr6:15211134..15212756-chr6:15293351..15295154,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10949291	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10949292	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10949293	0.80[ASN][1000 genomes]
rs10949295	0.85[AMR][1000 genomes]
rs11759828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11759847	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192599	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198694	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12199895	0.80[ASN][1000 genomes]
rs12201889	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12204124	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12206745	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12209228	0.90[ASN][1000 genomes]
rs12209453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12209539	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12209748	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12210592	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12212013	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12214719	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12215596	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12215740	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17575737	0.85[AMR][1000 genomes]
rs17619838	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17637773	0.85[AMR][1000 genomes]
rs17687211	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17713010	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28505073	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55634912	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55980198	0.90[ASN][1000 genomes]
rs6902997	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6919296	0.85[ASN][1000 genomes]
rs6935879	0.85[ASN][1000 genomes]
rs6938919	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72834551	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72834590	0.93[AMR][1000 genomes]
rs7765425	0.90[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	nsv1027010	chr6:15201803-15425629	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1030558	chr6:15234675-15449137	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv538142	chr6:15243960-15404893	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv601006	chr6:15275305-15300590	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv949448	chr6:15279490-15449441	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv1025512	chr6:15291551-15452395	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv538143	chr6:15291551-15452395	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15281400-15296400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr6:15281800-15300200	Weak transcription	Fetal Stomach	stomach
3	chr6:15282400-15299400	Weak transcription	Fetal Intestine Small	intestine
4	chr6:15282600-15296400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr6:15285200-15296000	Weak transcription	Liver	Liver
6	chr6:15285200-15296400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:15285200-15299400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:15285200-15299400	Weak transcription	A549	lung
9	chr6:15285800-15299400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:15285800-15299800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:15286200-15296200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr6:15286400-15299400	Weak transcription	NHEK	skin
13	chr6:15286400-15299600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:15286800-15299200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:15288800-15299000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr6:15288800-15299600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr6:15289000-15299200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:15289400-15295000	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr6:15289400-15296000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr6:15289600-15299400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:15290000-15296000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:15290200-15295000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr6:15290200-15298200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:15290200-15298200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr6:15290200-15299000	Weak transcription	Osteobl	bone
26	chr6:15290200-15300400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:15290600-15297400	Weak transcription	Small Intestine	intestine
28	chr6:15290600-15298000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:15290600-15309400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr6:15290800-15296800	Weak transcription	Adipose Nuclei	Adipose
31	chr6:15290800-15298400	Weak transcription	HepG2	liver
32	chr6:15290800-15299400	Weak transcription	Hela-S3	cervix
33	chr6:15291400-15294800	Enhancers	Brain Hippocampus Middle	brain
34	chr6:15291400-15296000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr6:15291800-15295000	Enhancers	Spleen	Spleen
36	chr6:15291800-15299400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr6:15291800-15299600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr6:15292000-15298600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr6:15292000-15299200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:15292000-15299600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:15292000-15299600	Weak transcription	HSMM	muscle
42	chr6:15292000-15303600	Weak transcription	Ovary	ovary
43	chr6:15292600-15295200	Enhancers	GM12878-XiMat	blood
44	chr6:15292800-15295000	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr6:15292800-15295000	Enhancers	Left Ventricle	heart
46	chr6:15292800-15296200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:15292800-15296800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:15293000-15294800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:15293000-15295200	Enhancers	Right Atrium	heart
50	chr6:15293000-15295400	Enhancers	Primary hematopoietic stem cells	blood

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