Variant report

Variant	rs563784628
Chromosome Location	chr6:109760822-109760823
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:61)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr6:109760621-109763112	SK-N-SH	brain:	n/a	chr6:109762145-109762160 chr6:109761832-109761847
2	FOSL2	chr6:109760677-109761114	A549	lung:	n/a	n/a
3	JUND	chr6:109760643-109761063	K562	blood:	n/a	n/a
4	MXI1	chr6:109760770-109762521	Hela-S3	cervix:	n/a	chr6:109762145-109762160 chr6:109761832-109761847
5	RFX5	chr6:109760761-109761111	Hela-S3	cervix:	n/a	n/a
6	RCOR1	chr6:109760772-109761288	Hela-S3	cervix:	n/a	n/a
7	FOSL1	chr6:109760679-109761003	K562	blood:	n/a	n/a
8	FOS	chr6:109760742-109761192	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr6:109759972-109762988	MCF10A-Er-Src	breast:	n/a	n/a
10	JUN	chr6:109760673-109761236	K562	blood:	n/a	n/a
11	POLR2A	chr6:109760757-109761021	Hela-S3	cervix:	n/a	n/a
12	SMC3	chr6:109760785-109761144	Hela-S3	cervix:	n/a	n/a
13	MYC	chr6:109760685-109762935	A549	lung:	n/a	chr6:109761564-109761574 chr6:109762181-109762190
14	POLR2A	chr6:109760717-109762995	K562	blood:	n/a	n/a
15	JUND	chr6:109760662-109761105	Hela-S3	cervix:	n/a	n/a
16	RCOR1	chr6:109760703-109761016	K562	blood:	n/a	n/a
17	SMARCB1	chr6:109760655-109762903	Hela-S3	cervix:	n/a	n/a
18	TEAD4	chr6:109760734-109761236	K562	blood:	n/a	n/a
19	POLR2A	chr6:109760694-109762951	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr6:109760732-109761173	Hela-S3	cervix:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:109760819-109760869	AG04449	skin:	fetal
2	chr6:109760819-109760869	ProgFib	skin:	n/a
3	chr6:109760819-109760869	HepG2	liver:	n/a
4	chr6:109760819-109760869	HIPEpiC	eye:	n/a
5	chr6:109760819-109760869	ECC-1	luminal epithelium:	n/a
6	chr6:109760819-109760869	MCF-7	breast:	n/a
7	chr6:109760819-109760869	CMK	blood:	n/a
8	chr6:109760819-109760869	Jurkat	blood:	n/a
9	chr6:109760819-109760869	AoSMC	blood vessel:	n/a
10	chr6:109760819-109760869	NH-A	brain:	n/a
11	chr6:109760819-109760869	NHDF-neo	bronchial:	n/a
12	chr6:109760819-109760869	GM12878	blood:	n/a
13	chr6:109760819-109760869	NT2-D1	testis:	n/a
14	chr6:109760819-109760869	ovcar-3	ovarian:	n/a
15	chr6:109760819-109760869	SK-N-SH_RA	brain:	n/a
16	chr6:109760819-109760869	PrEC	prostate:	n/a
17	chr6:109760819-109760869	AG09319	gingival:	n/a
18	chr6:109760819-109760869	HUVEC	blood vessel:	n/a
19	chr6:109760819-109760869	HEK293	kidney:	embryo
20	chr6:109760819-109760869	LNCaP	prostate:	n/a
21	chr6:109760819-109760869	Hela-S3	cervix:	n/a
22	chr6:109760819-109760869	HL-60	blood:	n/a
23	chr6:109760819-109760869	A549	lung:	n/a
24	chr6:109760819-109760869	AG09309	skin:	n/a
25	chr6:109760819-109760869	PANC-1	pancreas:	n/a
26	chr6:109760819-109760869	SAEC	small airway:	n/a
27	chr6:109760819-109760869	AG04450	lung:	fetal
28	chr6:109760819-109760869	Caco-2	colon:	n/a
29	chr6:109760819-109760869	NHBE	bronchial:	n/a
30	chr6:109760819-109760869	K562	blood:	n/a
31	chr6:109760819-109760869	HRE	kidney:	n/a
32	chr6:109760819-109760869	H1-hESC	embryonic stem cell:	embryo
33	chr6:109760819-109760869	GM06990	blood:	n/a
34	chr6:109760819-109760869	T-47D	breast:	n/a
35	chr6:109760819-109760869	Hepatocyte	liver:	n/a
36	chr6:109760819-109760869	HCPEpiC	choroid plexus:	n/a
37	chr6:109760819-109760869	HCF	heart:	n/a
38	chr6:109760819-109760869	BJ	skin:	n/a
39	chr6:109760819-109760869	GM19239	blood:	n/a
40	chr6:109760819-109760869	HMEC	breast:	n/a
41	chr6:109760819-109760869	HAEpiC	amniotic membrane:	n/a
42	chr6:109760819-109760869	GM12891	blood:	n/a
43	chr6:109760819-109760869	HPAEpiC	pulmonary alveolar:	n/a
44	chr6:109760819-109760869	U87	brain:	n/a
45	chr6:109760819-109760869	RPTEC	kidney:	n/a
46	chr6:109760819-109760869	HCM	heart:	n/a
47	chr6:109760819-109760869	AG10803	skin:	n/a
48	chr6:109760819-109760869	HEEpiC	esophagus:	n/a
49	chr6:109760819-109760869	HNPCEpiC	eye:	n/a
50	chr6:109760819-109760869	HRPEpiC	eye:	n/a

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:109747606..109757389-chr6:109757828..109761794,11	K562	blood:
2	chr6:109415348..109417479-chr6:109760287..109762549,2	K562	blood:
3	chr6:109702383..109706611-chr6:109760202..109762116,4	K562	blood:
4	chr6:109759652..109764361-chr6:109800705..109806354,8	K562	blood:
5	chr6:109414651..109418067-chr6:109760738..109763991,4	MCF-7	breast:
6	chr6:109702022..109707287-chr6:109760251..109763953,8	MCF-7	breast:
7	chr6:109760182..109762059-chr6:109802883..109805670,2	MCF-7	breast:
8	chr6:109759628..109764398-chr6:109803414..109806709,4	K562	blood:
9	chr6:109702065..109705528-chr6:109760483..109765471,8	MCF-7	breast:
10	chr6:109747606..109750215-chr6:109758639..109760987,2	K562	blood:
11	chr6:109760146..109763576-chr6:109804047..109805770,3	MCF-7	breast:
12	chr6:109752212..109757242-chr6:109759553..109764133,7	MCF-7	breast:

No data

Variant related genes	Relation type
SMPD2	TF binding region
SMPD2	CpG island
ENSG00000135535	Chromatin interaction
ENSG00000183137	Chromatin interaction
ENSG00000112365	Chromatin interaction
ENSG00000260273	Chromatin interaction
ENSG00000239160	Chromatin interaction
ENSG00000185250	Chromatin interaction
ENSG00000080546	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

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	nsv823818	chr6:109757222-109761294	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
2	esv3344959	chr6:109760484-109763032	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	9 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	chr6:109751200-109761400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:109756800-109761400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:109760200-109761600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
4	chr6:109760200-109763200	Active TSS	A549	lung
5	chr6:109760400-109761000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:109760400-109761600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:109760400-109762400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:109760400-109762400	Active TSS	Duodenum Mucosa	Duodenum
9	chr6:109760400-109762600	Active TSS	Ovary	ovary
10	chr6:109760400-109762600	Active TSS	Rectal Smooth Muscle	rectum
11	chr6:109760400-109762800	Active TSS	Fetal Intestine Small	intestine
12	chr6:109760400-109763400	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr6:109760600-109761000	Enhancers	Primary B cells from cord blood	blood
14	chr6:109760600-109761000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:109760600-109761000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr6:109760600-109761000	Enhancers	Fetal Thymus	thymus
17	chr6:109760600-109761200	Enhancers	Primary B cells from peripheral blood	blood
18	chr6:109760600-109761200	Enhancers	Primary T cells fromperipheralblood	blood
19	chr6:109760600-109761200	Flanking Active TSS	Fetal Brain Female	brain
20	chr6:109760600-109761200	Flanking Active TSS	HSMMtube	muscle
21	chr6:109760600-109761200	Flanking Active TSS	Osteobl	bone
22	chr6:109760600-109761400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:109760600-109761400	Flanking Active TSS	Placenta	Placenta
24	chr6:109760600-109761400	Flanking Active TSS	HSMM	muscle
25	chr6:109760600-109761400	Flanking Active TSS	NHEK	skin
26	chr6:109760600-109761600	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr6:109760600-109762400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:109760600-109762400	Active TSS	Colonic Mucosa	Colon
29	chr6:109760600-109762600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr6:109760600-109762600	Active TSS	Aorta	Aorta
31	chr6:109760600-109762600	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr6:109760600-109762600	Active TSS	Fetal Intestine Large	intestine
33	chr6:109760600-109762800	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr6:109760800-109761000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
35	chr6:109760800-109761000	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr6:109760800-109761000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
37	chr6:109760800-109761000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:109760800-109761000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
39	chr6:109760800-109761000	Enhancers	Primary T cells from cord blood	blood
40	chr6:109760800-109761000	Enhancers	Primary hematopoietic stem cells	blood
41	chr6:109760800-109761000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr6:109760800-109761000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr6:109760800-109761000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr6:109760800-109761000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr6:109760800-109761000	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr6:109760800-109761000	Flanking Active TSS	Brain Substantia Nigra	brain
47	chr6:109760800-109761000	Flanking Active TSS	Fetal Muscle Trunk	muscle
48	chr6:109760800-109761000	Enhancers	Placenta Amnion	Placenta Amnion
49	chr6:109760800-109761000	Enhancers	Psoas Muscle	Psoas
50	chr6:109760800-109761000	Enhancers	Stomach Smooth Muscle	stomach

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