Variant report

Variant	rs62411454
Chromosome Location	chr6:55965895-55965896
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:55964932..55967397-chr6:55975389..55977144,2	MCF-7	breast:
2	chr22:21977904..21980225-chr6:55963610..55966434,2	MCF-7	breast:

Extended variants
information (count: 159 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:155)

rs_ID	r²[population]
rs10456719	1.00[ASN][1000 genomes]
rs10484705	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10484706	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10484707	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10484708	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10807507	0.83[AFR][1000 genomes]
rs10807508	0.83[AFR][1000 genomes]
rs10807509	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1156708	1.00[ASN][1000 genomes]
rs12154070	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190240	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190695	0.80[AFR][1000 genomes]
rs12190930	0.81[AFR][1000 genomes]
rs12192012	0.84[AFR][1000 genomes]
rs12192490	0.83[AFR][1000 genomes]
rs12192902	0.86[AFR][1000 genomes]
rs12193215	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12193262	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193911	0.86[AFR][1000 genomes]
rs12194192	0.86[AFR][1000 genomes]
rs12194691	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12194733	0.86[AFR][1000 genomes]
rs12194916	0.80[AFR][1000 genomes]
rs12194997	0.86[AFR][1000 genomes]
rs12195034	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195340	0.86[AFR][1000 genomes]
rs12196038	0.82[AFR][1000 genomes]
rs12196208	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12196526	0.86[AFR][1000 genomes]
rs12196632	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12196649	0.80[AFR][1000 genomes]
rs12196860	0.83[AFR][1000 genomes]
rs12197715	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197951	0.80[AFR][1000 genomes]
rs12198225	0.80[AFR][1000 genomes]
rs12198686	0.86[AFR][1000 genomes]
rs12199385	0.83[AFR][1000 genomes]
rs12200110	1.00[ASN][1000 genomes]
rs12200525	0.80[AFR][1000 genomes]
rs12200667	0.81[AFR][1000 genomes]
rs12200716	1.00[ASN][1000 genomes]
rs12201639	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202221	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202885	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202972	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203653	0.86[AFR][1000 genomes]
rs12203768	0.86[AFR][1000 genomes]
rs12203971	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204789	0.80[AFR][1000 genomes]
rs12204894	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205903	0.85[AFR][1000 genomes]
rs12206360	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206617	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206920	0.86[AFR][1000 genomes]
rs12207093	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12207333	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12207447	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12207611	0.81[AFR][1000 genomes]
rs12207650	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12207715	0.86[AFR][1000 genomes]
rs12208804	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208823	0.86[AFR][1000 genomes]
rs12209192	0.86[AFR][1000 genomes]
rs12209420	0.80[AFR][1000 genomes]
rs12209422	1.00[ASN][1000 genomes]
rs12209452	1.00[ASN][1000 genomes]
rs12209509	0.86[AFR][1000 genomes]
rs12210402	0.80[AFR][1000 genomes]
rs12211223	0.86[AFR][1000 genomes]
rs12211939	1.00[ASN][1000 genomes]
rs12212135	0.85[AFR][1000 genomes]
rs12212143	0.86[AFR][1000 genomes]
rs12212998	0.80[AFR][1000 genomes]
rs12213291	0.86[AFR][1000 genomes]
rs12213571	0.86[AFR][1000 genomes]
rs12214023	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214519	0.86[AFR][1000 genomes]
rs12214559	0.83[AFR][1000 genomes]
rs12214662	0.86[AFR][1000 genomes]
rs12214985	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12216230	1.00[ASN][1000 genomes]
rs12216252	1.00[ASN][1000 genomes]
rs17218770	0.80[AFR][1000 genomes]
rs17221418	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17222493	1.00[ASN][1000 genomes]
rs17683841	0.80[AFR][1000 genomes]
rs17683955	0.86[AFR][1000 genomes]
rs17751085	0.80[AFR][1000 genomes]
rs17751143	0.80[AFR][1000 genomes]
rs17821163	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1925146	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1925150	1.00[ASN][1000 genomes]
rs1925151	1.00[ASN][1000 genomes]
rs1925168	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1925183	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764061	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2840999	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28452747	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2876629	0.81[AFR][1000 genomes]
rs34910254	0.86[AFR][1000 genomes]
rs4326238	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4336432	0.80[AFR][1000 genomes]
rs4388288	0.80[AFR][1000 genomes]
rs4544908	0.80[AFR][1000 genomes]
rs61200368	0.80[AFR][1000 genomes]
rs61465988	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61524954	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62404861	0.80[AFR][1000 genomes]
rs62404862	0.80[AFR][1000 genomes]
rs62404863	0.80[AFR][1000 genomes]
rs62404865	0.83[AFR][1000 genomes]
rs62404866	0.86[AFR][1000 genomes]
rs62404867	0.86[AFR][1000 genomes]
rs62404868	0.86[AFR][1000 genomes]
rs62404869	0.86[AFR][1000 genomes]
rs62404893	0.86[AFR][1000 genomes]
rs62404894	0.82[AFR][1000 genomes]
rs62404895	0.86[AFR][1000 genomes]
rs62404896	0.86[AFR][1000 genomes]
rs62404897	0.86[AFR][1000 genomes]
rs62404898	0.86[AFR][1000 genomes]
rs62404900	0.83[AFR][1000 genomes]
rs62406155	0.80[AFR][1000 genomes]
rs62406156	0.80[AFR][1000 genomes]
rs62406157	0.80[AFR][1000 genomes]
rs62411452	0.86[AFR][1000 genomes]
rs62411453	0.86[AFR][1000 genomes]
rs62411455	0.86[AFR][1000 genomes]
rs62411457	0.86[AFR][1000 genomes]
rs62411866	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411869	1.00[ASN][1000 genomes]
rs62411870	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62412798	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62412799	0.81[AFR][1000 genomes]
rs62412802	1.00[ASN][1000 genomes]
rs62413463	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413464	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413466	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413468	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413482	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413546	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62413548	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62413549	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413552	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413553	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413554	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413555	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742633	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751644	1.00[ASN][1000 genomes]
rs7770267	1.00[ASN][1000 genomes]
rs7771018	1.00[ASN][1000 genomes]
rs885631	1.00[ASN][1000 genomes]
rs9296811	1.00[ASN][1000 genomes]
rs990188	1.00[ASN][1000 genomes]
rs990189	1.00[ASN][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	nsv1034037	chr6:55222409-56069600	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv885911	chr6:55789704-56143231	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv526703	chr6:55810482-56023811	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv1029182	chr6:55910866-55991956	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55920600-56018400	Weak transcription	Ovary	ovary
2	chr6:55956600-55978400	Weak transcription	Aorta	Aorta
3	chr6:55959600-55969600	Weak transcription	Fetal Lung	lung
4	chr6:55960600-55977800	Weak transcription	Fetal Muscle Leg	muscle
5	chr6:55960600-55978000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr6:55961400-55969600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr6:55962200-55977200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr6:55963800-55967400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr6:55964200-55967200	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr6:55964400-55966800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:55964400-55968000	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr6:55964800-55967800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:55965200-55967400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:55965200-55967600	Enhancers	NHDF-Ad	bronchial
15	chr6:55965200-55967800	Enhancers	Muscle Satellite Cultured Cells	--
16	chr6:55965400-55966600	Enhancers	NH-A	brain
17	chr6:55965400-55967400	Enhancers	HSMMtube	muscle
18	chr6:55965600-55966400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:55965600-55966400	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr6:55965600-55966400	Enhancers	NHEK	skin
21	chr6:55965600-55966600	Enhancers	NHLF	lung
22	chr6:55965600-55967200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:55965600-55967400	Enhancers	Hela-S3	cervix
24	chr6:55965600-55967400	Enhancers	HSMM	muscle
25	chr6:55965600-55967400	Enhancers	Osteobl	bone
26	chr6:55965600-55967800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:55965800-55966000	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr6:55965800-55966200	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr6:55965800-55966200	Flanking Active TSS	A549	lung
30	chr6:55965800-55966400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:55965800-55966400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:55965800-55966400	Enhancers	HUVEC	blood vessel

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