Variant report

Variant	rs9462495
Chromosome Location	chr6:39197482-39197483
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:39197400-39197550	NHEK	skin:	n/a	chr6:39197441-39197450
2	RAD21	chr6:39197176-39197679	H1-hESC	embryonic stem cell:	n/a	chr6:39197296-39197308
3	USF2	chr6:39196998-39197573	Hela-S3	cervix:	n/a	n/a
4	RAD21	chr6:39197265-39197577	SK-N-SH_RA	brain:	n/a	chr6:39197296-39197308
5	CTCF	chr6:39197227-39197588	MCF-7	breast:	n/a	chr6:39197441-39197450
6	TBL1XR1	chr6:39197015-39197645	K562	blood:	n/a	n/a
7	CTCF	chr6:39197380-39197530	AG09309	skin:	n/a	chr6:39197441-39197450
8	POLR2A	chr6:39195484-39197676	K562	blood:	n/a	n/a
9	E2F4	chr6:39196763-39197633	MCF10A-Er-Src	breast:	n/a	chr6:39197253-39197262
10	CTCF	chr6:39197360-39197510	GM12864	blood:	n/a	chr6:39197441-39197450
11	EP300	chr6:39196902-39197875	K562	blood:	n/a	chr6:39197253-39197262 chr6:39197457-39197466 chr6:39197338-39197347
12	CTCF	chr6:39197360-39197510	GM12867	blood:	n/a	chr6:39197441-39197450
13	CTCF	chr6:39197204-39197686	K562	blood:	n/a	chr6:39197441-39197450
14	CTCF	chr6:39197211-39197581	Pancreas_OC	pancreas:	n/a	chr6:39197441-39197450
15	CTCF	chr6:39197331-39197547	SK-N-SH_RA	brain:	n/a	chr6:39197441-39197450
16	MAX	chr6:39196876-39197666	H1-hESC	embryonic stem cell:	n/a	chr6:39197195-39197205 chr6:39197196-39197207 chr6:39197199-39197208
17	CTCF	chr6:39197355-39197544	ProgFib	skin:	n/a	chr6:39197441-39197450
18	STAT3	chr6:39197156-39197538	MCF10A-Er-Src	breast:	n/a	n/a
19	E2F6	chr6:39196958-39197605	H1-hESC	embryonic stem cell:	n/a	chr6:39197163-39197174 chr6:39197253-39197262
20	CTCF	chr6:39197400-39197550	GM12870	blood:	n/a	chr6:39197441-39197450
21	RUNX3	chr6:39197341-39197560	GM12878	blood:	n/a	n/a
22	CTCF	chr6:39197420-39197570	NHDF-neo	bronchial:	n/a	chr6:39197441-39197450
23	CTCF	chr6:39197360-39197510	GM12872	blood:	n/a	chr6:39197441-39197450
24	PML	chr6:39196772-39197741	K562	blood:	n/a	chr6:39196910-39196918
25	CTCF	chr6:39196971-39197910	A549	lung:	n/a	chr6:39197441-39197450
26	MAX	chr6:39195529-39197639	NB4	blood:	n/a	chr6:39197195-39197205 chr6:39197196-39197207 chr6:39197199-39197208
27	GTF2F1	chr6:39197096-39197507	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr6:39197322-39197550	Lung_OC	lung:	n/a	chr6:39197441-39197450
29	RAD21	chr6:39197078-39197733	H1-hESC	embryonic stem cell:	n/a	chr6:39197296-39197308
30	TEAD4	chr6:39196864-39197575	K562	blood:	n/a	n/a
31	POLR2A	chr6:39196017-39197575	PBDE	blood:	n/a	n/a
32	E2F1	chr6:39196836-39197587	Hela-S3	cervix:	n/a	chr6:39197253-39197262
33	ATF3	chr6:39197073-39197567	H1-hESC	embryonic stem cell:	n/a	chr6:39197251-39197260
34	E2F4	chr6:39196752-39197634	K562	blood:	n/a	chr6:39197253-39197262
35	CTCF	chr6:39197277-39197580	H1-hESC	embryonic stem cell:	n/a	chr6:39197441-39197450
36	CTCF	chr6:39197420-39197570	HL-60	blood:	n/a	chr6:39197441-39197450
37	ZMIZ1	chr6:39196725-39197618	K562	blood:	n/a	n/a
38	ZNF143	chr6:39197165-39197645	H1-hESC	embryonic stem cell:	n/a	chr6:39197281-39197291 chr6:39197252-39197262
39	CTCF	chr6:39197354-39197548	LNCaP	prostate:	n/a	chr6:39197441-39197450
40	CTCF	chr6:39197360-39197510	HUVEC	blood vessel:	n/a	chr6:39197441-39197450
41	CREB1	chr6:39196874-39197596	K562	blood:	n/a	n/a
42	CTCF	chr6:39197400-39197550	GM12868	blood:	n/a	chr6:39197441-39197450
43	POLR2A	chr6:39195050-39197641	K562	blood:	n/a	n/a
44	CTCF	chr6:39197373-39197518	Medullo	brain:	n/a	chr6:39197441-39197450
45	CTCF	chr6:39197400-39197550	HMF	breast:	n/a	chr6:39197441-39197450
46	CTCF	chr6:39197420-39197710	HVMF	connective:	n/a	chr6:39197441-39197450
47	CTCF	chr6:39197400-39197550	SAEC	small airway:	n/a	chr6:39197441-39197450
48	EGR1	chr6:39196753-39197743	HCT-116	colon:	n/a	chr6:39197258-39197271 chr6:39196947-39196957 chr6:39197252-39197262 chr6:39197421-39197431 chr6:39197258-39197271 chr6:39197253-39197275 chr6:39197258-39197271 chr6:39197255-39197269 chr6:39197258-39197271 chr6:39197259-39197269 chr6:39197259-39197270
49	CTCF	chr6:39197360-39197510	AG10803	skin:	n/a	chr6:39197441-39197450
50	TBP	chr6:39195934-39197832	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:39195950..39197614-chr6:39288788..39290950,2	K562	blood:
2	chr6:39197274..39197830-chr6:39269306..39269922,2	K562	blood:
3	chr6:39081916..39085282-chr6:39194692..39197671,3	K562	blood:
4	chr6:39081916..39083618-chr6:39195475..39198026,2	K562	blood:

Variant related genes	Relation type
KCNK5	TF binding region
ENSG00000112167	Chromatin interaction
ENSG00000095981	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs2395715	1.00[AFR][1000 genomes]
rs2561402	1.00[CEU][hapmap];0.91[ASN][1000 genomes]
rs9462488	1.00[AFR][1000 genomes]
rs9462518	1.00[AFR][1000 genomes]
rs9462519	1.00[AFR][1000 genomes]
rs9462520	1.00[AFR][1000 genomes]
rs9471005	1.00[AFR][1000 genomes]
rs9471011	1.00[AFR][1000 genomes]
rs9471013	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.91[ASN][1000 genomes]
rs9471016	0.91[ASN][1000 genomes]
rs9471017	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9471026	1.00[AFR][1000 genomes]
rs9471037	1.00[AFR][1000 genomes]
rs9471047	1.00[AFR][1000 genomes]
rs9471049	1.00[AFR][1000 genomes]
rs9471052	1.00[AFR][1000 genomes]
rs9471053	1.00[AFR][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	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39193800-39197800	Flanking Active TSS	Fetal Thymus	thymus
2	chr6:39194800-39197600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:39195200-39197600	Bivalent/Poised TSS	Stomach Mucosa	stomach
4	chr6:39195200-39197800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr6:39195200-39197800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:39195200-39197800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:39195800-39197600	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr6:39195800-39197600	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr6:39195800-39197600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr6:39195800-39197600	Active TSS	K562	blood
11	chr6:39195800-39197800	Active TSS	H9 Cell Line	embryonic stem cell
12	chr6:39195800-39197800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr6:39195800-39197800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr6:39196000-39197600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr6:39196000-39197600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
16	chr6:39196000-39197600	Active TSS	Ovary	ovary
17	chr6:39196000-39197600	Flanking Active TSS	Thymus	Thymus
18	chr6:39196000-39197800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
19	chr6:39196000-39198000	Active TSS	Rectal Smooth Muscle	rectum
20	chr6:39196200-39197600	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
21	chr6:39196200-39197600	Active TSS	HSMM	muscle
22	chr6:39196200-39197800	Active TSS	A549	lung
23	chr6:39196400-39197800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
24	chr6:39196400-39198000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr6:39196600-39197600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:39196600-39197600	Active TSS	Brain Substantia Nigra	brain
27	chr6:39196800-39197600	Active TSS	H1 Cell Line	embryonic stem cell
28	chr6:39196800-39197600	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr6:39196800-39197600	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr6:39196800-39197600	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:39196800-39197600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
32	chr6:39196800-39197600	Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr6:39196800-39197600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:39196800-39197600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:39196800-39197600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:39196800-39197600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
37	chr6:39196800-39197600	Bivalent/Poised TSS	Fetal Brain Female	brain
38	chr6:39196800-39197600	Active TSS	Fetal Intestine Large	intestine
39	chr6:39196800-39197600	Active TSS	Fetal Lung	lung
40	chr6:39196800-39197600	Flanking Active TSS	Placenta	Placenta
41	chr6:39196800-39197600	Active TSS	Psoas Muscle	Psoas
42	chr6:39196800-39197600	Active TSS	Hela-S3	cervix
43	chr6:39196800-39197600	Flanking Active TSS	HMEC	breast
44	chr6:39196800-39197600	Bivalent/Poised TSS	NHLF	lung
45	chr6:39196800-39197800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:39196800-39197800	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr6:39196800-39198000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr6:39197000-39197600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
49	chr6:39197000-39197600	Active TSS	Brain Anterior Caudate	brain
50	chr6:39197000-39197600	Active TSS	Brain Cingulate Gyrus	brain

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