Variant report

Variant	rs62405965
Chromosome Location	chr6:80719784-80719785
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:80718444..80720486-chr6:80838754..80840605,2	K562	blood:
2	chr6:80719003..80721359-chr6:80737643..80739358,2	K562	blood:
3	chr6:80649918..80652477-chr6:80718505..80720470,2	K562	blood:
4	chr6:80714432..80716349-chr6:80717842..80720279,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112742	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12524658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12528075	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12528948	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12529133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1550035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17174951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17175251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17176133	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17254389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17254634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1801460	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1801465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4547972	0.81[EUR][1000 genomes]
rs45495802	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4613770	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4642425	0.81[EUR][1000 genomes]
rs55956173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56219628	0.80[EUR][1000 genomes]
rs56302322	0.81[EUR][1000 genomes]
rs62405967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62405994	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62405995	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62405997	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62405999	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62406015	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62406016	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7765797	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7769377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv5370	chr6:80715351-80751740	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80714800-80738800	Weak transcription	Small Intestine	intestine
2	chr6:80715000-80730400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:80715000-80748000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:80715000-80752200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:80715000-80752400	Weak transcription	Placenta	Placenta
6	chr6:80715200-80721200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:80715200-80726000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:80715200-80727000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr6:80715200-80730800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:80715200-80734000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr6:80715200-80734400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:80715200-80739200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr6:80715200-80749600	Weak transcription	Fetal Intestine Small	intestine
14	chr6:80715200-80752000	Weak transcription	Primary B cells from cord blood	blood
15	chr6:80715200-80752200	Weak transcription	Primary T cells from cord blood	blood
16	chr6:80715400-80721200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr6:80715400-80721200	Weak transcription	Fetal Kidney	kidney
18	chr6:80715400-80722600	Weak transcription	Fetal Intestine Large	intestine
19	chr6:80715400-80726000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:80715400-80727000	Weak transcription	Fetal Muscle Leg	muscle
21	chr6:80715400-80729400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr6:80715400-80742200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:80715400-80743200	Weak transcription	Brain Germinal Matrix	brain
24	chr6:80715400-80745400	Weak transcription	Fetal Lung	lung
25	chr6:80715400-80755000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr6:80715400-80756800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:80715600-80720200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr6:80715600-80721200	Weak transcription	Osteobl	bone
29	chr6:80715600-80724600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr6:80715600-80725200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:80715600-80739200	Weak transcription	Fetal Stomach	stomach
32	chr6:80715600-80754400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr6:80715600-80763800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr6:80715800-80720800	Weak transcription	NHDF-Ad	bronchial
35	chr6:80715800-80733400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:80715800-80753600	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr6:80715800-80753800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr6:80715800-80754400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr6:80716000-80723000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:80716000-80726000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:80716000-80728600	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr6:80716000-80729400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:80716000-80739200	Weak transcription	NHEK	skin
44	chr6:80716000-80743600	Weak transcription	Fetal Heart	heart
45	chr6:80716200-80725200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr6:80716200-80727800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:80716200-80728000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr6:80716200-80754600	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr6:80716400-80720400	Weak transcription	Hela-S3	cervix
50	chr6:80716400-80727800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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