Variant report

Variant	rs1372570
Chromosome Location	chr6:46293601-46293602
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	JUND	chr6:46293357-46293615	HepG2	liver:	n/a	chr6:46293585-46293592 chr6:46293434-46293443 chr6:46293584-46293592 chr6:46293584-46293592
2	KAP1	chr6:46293103-46294058	U2OS	brain:	n/a	n/a
3	REST	chr6:46292798-46294411	H1-neurons	neurons:	n/a	chr6:46293305-46293319 chr6:46294013-46294022
4	FOS	chr6:46293416-46293791	MCF10A-Er-Src	breast:	n/a	chr6:46293585-46293592 chr6:46293434-46293443 chr6:46293584-46293592 chr6:46293584-46293592
5	STAT3	chr6:46293413-46293779	MCF10A-Er-Src	breast:	n/a	n/a
6	RUNX3	chr6:46293480-46293788	GM12878	blood:	n/a	n/a
7	FOS	chr6:46293466-46293771	MCF10A-Er-Src	breast:	n/a	chr6:46293585-46293592 chr6:46293584-46293592 chr6:46293584-46293592
8	STAT3	chr6:46293513-46293717	MCF10A-Er-Src	breast:	n/a	n/a
9	TCF7L2	chr6:46293256-46294038	HEK293	kidney:	n/a	chr6:46293484-46293498
10	KAP1	chr6:46293112-46294150	HEK293	kidney:	n/a	n/a
11	ATF2	chr6:46293171-46293628	H1-hESC	embryonic stem cell:	n/a	n/a
12	FOS	chr6:46293484-46293740	MCF10A-Er-Src	breast:	n/a	chr6:46293585-46293592 chr6:46293584-46293592 chr6:46293584-46293592
13	POLR2A	chr6:46292966-46294191	H1-neurons	neurons:	n/a	n/a
14	JUND	chr6:46293337-46293703	H1-hESC	embryonic stem cell:	n/a	chr6:46293585-46293592 chr6:46293434-46293443 chr6:46293584-46293592 chr6:46293584-46293592
15	MAFK	chr6:46293558-46293650	HepG2	liver:	n/a	chr6:46293610-46293627
16	STAT3	chr6:46293389-46293784	MCF10A-Er-Src	breast:	n/a	n/a
17	ATF2	chr6:46293218-46293607	H1-hESC	embryonic stem cell:	n/a	n/a
18	FOS	chr6:46293415-46293765	MCF10A-Er-Src	breast:	n/a	chr6:46293585-46293592 chr6:46293434-46293443 chr6:46293584-46293592 chr6:46293584-46293592
19	POLR2A	chr6:46293187-46294312	H1-neurons	neurons:	n/a	n/a
20	EP300	chr6:46293380-46293673	SK-N-SH_RA	brain:	n/a	chr6:46293583-46293592
21	POLR2A	chr6:46293586-46293781	MCF10A-Er-Src	breast:	n/a	n/a
22	EP300	chr6:46293422-46293784	SK-N-SH_RA	brain:	n/a	chr6:46293583-46293592 chr6:46293741-46293750
23	MYC	chr6:46293592-46293684	MCF10A-Er-Src	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:46293571-46293621	SKMC	muscle:	n/a
2	chr6:46293571-46293621	HEK293	kidney:	embryo
3	chr6:46293571-46293621	SK-N-SH	brain:	n/a
4	chr6:46293571-46293621	SK-N-MC	brain:	n/a
5	chr6:46293571-46293621	GM12892	blood:	n/a
6	chr6:46293571-46293621	HCM	heart:	n/a
7	chr6:46293571-46293621	HRPEpiC	eye:	n/a
8	chr6:46293571-46293621	Hela-S3	cervix:	n/a
9	chr6:46293571-46293621	ECC-1	luminal epithelium:	n/a
10	chr6:46293571-46293621	ProgFib	skin:	n/a
11	chr6:46293571-46293621	MCF-7	breast:	n/a
12	chr6:46293571-46293621	AoSMC	blood vessel:	n/a
13	chr6:46293571-46293621	AG09319	gingival:	n/a
14	chr6:46293571-46293621	NHBE	bronchial:	n/a
15	chr6:46293571-46293621	BE2_C	brain:	n/a
16	chr6:46293571-46293621	HIPEpiC	eye:	n/a
17	chr6:46293571-46293621	U87	brain:	n/a
18	chr6:46293571-46293621	HNPCEpiC	eye:	n/a
19	chr6:46293571-46293621	Caco-2	colon:	n/a
20	chr6:46293571-46293621	GM19239	blood:	n/a
21	chr6:46293571-46293621	AG04450	lung:	fetal
22	chr6:46293571-46293621	SAEC	small airway:	n/a
23	chr6:46293571-46293621	GM12878	blood:	n/a
24	chr6:46293571-46293621	HCT-116	colon:	n/a
25	chr6:46293571-46293621	AG04449	skin:	fetal
26	chr6:46293571-46293621	HepG2	liver:	n/a
27	chr6:46293571-46293621	PrEC	prostate:	n/a
28	chr6:46293571-46293621	LNCaP	prostate:	n/a
29	chr6:46293571-46293621	T-47D	breast:	n/a
30	chr6:46293571-46293621	NHDF-neo	bronchial:	n/a
31	chr6:46293571-46293621	NB4	blood:	n/a
32	chr6:46293571-46293621	ovcar-3	ovarian:	n/a
33	chr6:46293571-46293621	PFSK-1	brain:	n/a
34	chr6:46293571-46293621	HCF	heart:	n/a
35	chr6:46293571-46293621	PANC-1	pancreas:	n/a
36	chr6:46293571-46293621	Jurkat	blood:	n/a
37	chr6:46293571-46293621	K562	blood:	n/a
38	chr6:46293571-46293621	HRCEpiC	kidney:	n/a
39	chr6:46293571-46293621	RPTEC	kidney:	n/a
40	chr6:46293571-46293621	HPAEpiC	pulmonary alveolar:	n/a
41	chr6:46293571-46293621	BJ	skin:	n/a
42	chr6:46293571-46293621	HCPEpiC	choroid plexus:	n/a
43	chr6:46293571-46293621	H1-hESC	embryonic stem cell:	embryo
44	chr6:46293571-46293621	GM06990	blood:	n/a
45	chr6:46293571-46293621	HL-60	blood:	n/a
46	chr6:46293571-46293621	HEEpiC	esophagus:	n/a
47	chr6:46293571-46293621	Hepatocyte	liver:	n/a
48	chr6:46293571-46293621	GM12891	blood:	n/a
49	chr6:46293571-46293621	NH-A	brain:	n/a
50	chr6:46293571-46293621	SK-N-SH_RA	brain:	n/a

Variant related genes	Relation type
RCAN2	TF binding region
RCAN2	CpG island

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1372571	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1442212	1.00[AMR][1000 genomes]
rs1442214	1.00[AMR][1000 genomes]
rs56893394	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57387297	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7766177	1.00[AMR][1000 genomes]
rs7772923	1.00[AMR][1000 genomes]
rs9463200	1.00[AMR][1000 genomes]
rs9472735	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830653	chr6:46277573-46434991	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:46283400-46295600	Weak transcription	Pancreas	Pancrea
2	chr6:46290400-46294000	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr6:46290600-46297600	Enhancers	Rectal Smooth Muscle	rectum
4	chr6:46290800-46294200	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr6:46291000-46294200	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr6:46291200-46293800	Active TSS	Brain Substantia Nigra	brain
7	chr6:46291200-46295800	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr6:46291400-46293800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:46291400-46294000	Active TSS	Brain Cingulate Gyrus	brain
10	chr6:46291800-46294200	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr6:46292000-46294800	Enhancers	Fetal Brain Male	brain
12	chr6:46292000-46297800	Enhancers	Fetal Lung	lung
13	chr6:46292200-46294200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr6:46292200-46294600	Weak transcription	Aorta	Aorta
15	chr6:46292400-46293800	Flanking Active TSS	HSMMtube	muscle
16	chr6:46292600-46293800	Flanking Active TSS	Fetal Brain Female	brain
17	chr6:46292600-46293800	Enhancers	Fetal Stomach	stomach
18	chr6:46292600-46294000	Flanking Active TSS	Brain Germinal Matrix	brain
19	chr6:46292800-46293800	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr6:46292800-46294200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:46293000-46293800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:46293000-46294000	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr6:46293000-46294200	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr6:46293000-46294200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:46293000-46294200	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr6:46293000-46294200	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr6:46293000-46294200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr6:46293000-46294200	Flanking Active TSS	NHDF-Ad	bronchial
29	chr6:46293000-46294600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:46293200-46293800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:46293200-46293800	Flanking Active TSS	HSMM	muscle
32	chr6:46293200-46294000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr6:46293200-46294000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr6:46293200-46294000	Enhancers	Osteobl	bone
35	chr6:46293200-46294200	Enhancers	H1 Cell Line	embryonic stem cell
36	chr6:46293200-46294200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:46293200-46294200	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr6:46293200-46294200	Enhancers	Primary T cells from cord blood	blood
39	chr6:46293200-46294200	Enhancers	Ovary	ovary
40	chr6:46293200-46294200	Enhancers	Right Ventricle	heart
41	chr6:46293400-46293800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr6:46293400-46293800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr6:46293400-46294000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
44	chr6:46293400-46294000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr6:46293400-46294000	Enhancers	Adipose Nuclei	Adipose
46	chr6:46293400-46294200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:46293400-46294200	Enhancers	Left Ventricle	heart
48	chr6:46293400-46294200	Enhancers	Right Atrium	heart
49	chr6:46293600-46293800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:46293600-46293800	Flanking Active TSS	Brain Angular Gyrus	brain

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