Variant report

Variant	rs6763560
Chromosome Location	chr3:156543706-156543707
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:263)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:263 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr3:156543641-156544832	H1-hESC	embryonic stem cell:	n/a	chr3:156544104-156544113
2	POLR2A	chr3:156543159-156545423	MCF10A-Er-Src	breast:	n/a	n/a
3	EP300	chr3:156543631-156544968	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:156543673-156544978	GM18951	blood:	n/a	n/a
5	POLR2A	chr3:156543327-156544811	HUVEC	blood vessel:	n/a	n/a
6	PAX5	chr3:156543691-156544917	GM12878	blood:	n/a	n/a
7	GATA3	chr3:156543631-156545128	A549	lung:	n/a	n/a
8	POLR2A	chr3:156543217-156545003	HUVEC	blood vessel:	n/a	n/a
9	NR2F2	chr3:156543599-156544935	MCF-7	breast:	n/a	n/a
10	POLR2A	chr3:156543056-156544874	GM12878	blood:	n/a	n/a
11	MAX	chr3:156543645-156544725	K562	blood:	n/a	chr3:156544061-156544070
12	POLR2A	chr3:156543240-156544979	Hela-S3	cervix:	n/a	n/a
13	ZKSCAN1	chr3:156543239-156544897	Hela-S3	cervix:	n/a	n/a
14	MAX	chr3:156543304-156544834	K562	blood:	n/a	chr3:156544061-156544070
15	HEY1	chr3:156543199-156544879	K562	blood:	n/a	n/a
16	POLR2A	chr3:156542971-156545221	Hela-S3	cervix:	n/a	n/a
17	MAX	chr3:156543225-156545079	A549	lung:	n/a	chr3:156544061-156544070
18	POLR2A	chr3:156543240-156544926	GM12878	blood:	n/a	n/a
19	RAD21	chr3:156543340-156544900	Hela-S3	cervix:	n/a	n/a
20	RAD21	chr3:156543683-156544086	H1-hESC	embryonic stem cell:	n/a	n/a
21	MAX	chr3:156543378-156544852	MCF-7	breast:	n/a	chr3:156544061-156544070
22	POLR2A	chr3:156543263-156544968	K562	blood:	n/a	n/a
23	CBX3	chr3:156543137-156544892	K562	blood:	n/a	n/a
24	YY1	chr3:156543685-156544887	A549	lung:	n/a	chr3:156544104-156544113
25	MYC	chr3:156543500-156544789	MCF10A-Er-Src	breast:	n/a	chr3:156544061-156544070
26	MAX	chr3:156543352-156544688	NB4	blood:	n/a	chr3:156544061-156544070
27	E2F6	chr3:156543323-156544810	K562	blood:	n/a	chr3:156544104-156544113
28	CTCF	chr3:156543680-156543830	HPF	lung:	n/a	n/a
29	PML	chr3:156543263-156544981	GM12878	blood:	n/a	n/a
30	CREB1	chr3:156543509-156544983	GM12878	blood:	n/a	chr3:156544069-156544082
31	EP300	chr3:156543312-156545124	GM12878	blood:	n/a	n/a
32	TAF1	chr3:156543677-156544492	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr3:156543617-156544772	Gliobla	brain:	n/a	n/a
34	POLR2A	chr3:156543636-156544867	MCF-7	breast:	n/a	n/a
35	RCOR1	chr3:156543281-156544999	K562	blood:	n/a	n/a
36	POLR2A	chr3:156543232-156544902	GM12891	blood:	n/a	n/a
37	TBL1XR1	chr3:156543429-156544772	K562	blood:	n/a	n/a
38	REST	chr3:156543506-156544773	H1-neurons	neurons:	n/a	chr3:156543867-156543876 chr3:156543863-156543876
39	POLR2A	chr3:156543653-156544389	SK-N-SH	brain:	n/a	n/a
40	ELK1	chr3:156543673-156544810	Hela-S3	cervix:	n/a	n/a
41	TAF1	chr3:156543669-156544359	GM12892	blood:	n/a	n/a
42	MXI1	chr3:156543381-156544988	GM12878	blood:	n/a	n/a
43	SMC3	chr3:156543273-156545193	Hela-S3	cervix:	n/a	n/a
44	TEAD4	chr3:156543700-156544157	H1-hESC	embryonic stem cell:	n/a	n/a
45	ZNF263	chr3:156543702-156544782	HEK293-T-REx	kidney:	n/a	n/a
46	CHD2	chr3:156543687-156544885	GM12878	blood:	n/a	n/a
47	ARID3A	chr3:156543256-156544114	K562	blood:	n/a	n/a
48	TAF1	chr3:156543634-156544871	A549	lung:	n/a	n/a
49	TCF7L2	chr3:156543396-156544851	HCT-116	colon:	n/a	chr3:156543512-156543521
50	REST	chr3:156543180-156545046	A549	lung:	n/a	chr3:156543867-156543876 chr3:156543863-156543876

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:156542707..156546513-chr3:156875626..156880471,4	K562	blood:
2	chr3:156398881..156401137-chr3:156542792..156545641,2	MCF-7	breast:
3	chr3:156268894..156273100-chr3:156541711..156545313,4	MCF-7	breast:
4	chr20:37101256..37102035-chr3:156543587..156544445,2	Hela-S3	cervix:
5	chr3:156543166..156544685-chr3:156806392..156807926,2	K562	blood:
6	chr3:156390293..156396385-chr3:156542364..156548172,18	MCF-7	breast:
7	chr12:123011046..123011728-chr3:156543598..156544566,2	NB4	blood:
8	chr3:156527949..156530289-chr3:156543460..156546861,3	K562	blood:
9	chr3:156390535..156395368-chr3:156542467..156546251,7	MCF-7	breast:
10	chr3:156527592..156531932-chr3:156540848..156546879,8	MCF-7	breast:
11	chr3:156543622..156545874-chr3:156870977..156873628,2	MCF-7	breast:
12	chr3:156398799..156400378-chr3:156543351..156545988,2	MCF-7	breast:
13	chr3:156542698..156545519-chr3:156890354..156893395,4	K562	blood:
14	chr17:7123187..7124006-chr3:156543455..156544032,2	Hela-S3	cervix:
15	chr3:156391796..156394617-chr3:156542307..156544876,4	K562	blood:
16	chr1:8085836..8086465-chr3:156543539..156544070,2	Hela-S3	cervix:
17	chr3:156543311..156544068-chr9:34329475..34330005,2	Hela-S3	cervix:
18	chr3:156543568..156544551-chr7:5569381..5570372,2	Hela-S3	cervix:
19	chr14:103988216..103989188-chr3:156543435..156544222,2	HCT-116	colon:
20	chr11:65271665..65272243-chr3:156543516..156544058,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
LEKR1	TF binding region
ENSG00000222675	Chromatin interaction
ENSG00000230457	Chromatin interaction
ENSG00000241135	Chromatin interaction
ENSG00000111011	Chromatin interaction
ENSG00000170471	Chromatin interaction
ENSG00000163659	Chromatin interaction
ENSG00000072778	Chromatin interaction
ENSG00000075624	Chromatin interaction
ENSG00000166165	Chromatin interaction
ENSG00000116285	Chromatin interaction
ENSG00000114850	Chromatin interaction
ENSG00000164978	Chromatin interaction
ENSG00000243176	Chromatin interaction
ENSG00000201778	Chromatin interaction
ENSG00000163660	Chromatin interaction
ENSG00000243926	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1991618	0.83[AFR][1000 genomes]
rs57472927	0.81[AFR][1000 genomes]
rs61607068	0.83[AFR][1000 genomes]
rs6763606	0.83[AFR][1000 genomes]
rs73873733	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7638335	0.85[AMR][1000 genomes]
rs9818849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9855517	0.81[AFR][1000 genomes]
rs9866769	0.83[AFR][1000 genomes]
rs9873640	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv877686	chr3:156489509-156557697	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156541800-156543800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:156543000-156545400	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr3:156543200-156543800	Flanking Active TSS	Fetal Kidney	kidney
4	chr3:156543200-156543800	Flanking Active TSS	Hela-S3	cervix
5	chr3:156543200-156544000	Flanking Active TSS	GM12878-XiMat	blood
6	chr3:156543200-156544000	Flanking Active TSS	K562	blood
7	chr3:156543200-156544600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:156543200-156544800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr3:156543200-156545000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:156543200-156545200	Active TSS	Primary T killer memory cells from peripheral blood	blood
11	chr3:156543200-156545200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:156543200-156545200	Flanking Active TSS	HUVEC	blood vessel
13	chr3:156543200-156545400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:156543400-156543800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
15	chr3:156543400-156543800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:156543400-156543800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr3:156543400-156543800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
18	chr3:156543400-156543800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:156543400-156543800	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr3:156543400-156543800	Flanking Active TSS	Brain Cingulate Gyrus	brain
21	chr3:156543400-156543800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
22	chr3:156543400-156543800	Flanking Active TSS	Fetal Heart	heart
23	chr3:156543400-156543800	Flanking Active TSS	Fetal Intestine Large	intestine
24	chr3:156543400-156543800	Flanking Active TSS	Fetal Muscle Leg	muscle
25	chr3:156543400-156543800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr3:156543400-156543800	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr3:156543400-156543800	Flanking Active TSS	A549	lung
28	chr3:156543400-156543800	Flanking Active TSS	HSMM	muscle
29	chr3:156543400-156543800	Flanking Active TSS	NHDF-Ad	bronchial
30	chr3:156543400-156543800	Flanking Active TSS	NHLF	lung
31	chr3:156543400-156544000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
32	chr3:156543400-156544000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr3:156543400-156544000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr3:156543400-156544000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:156543400-156544000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr3:156543400-156544000	Flanking Active TSS	Fetal Thymus	thymus
37	chr3:156543400-156544000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr3:156543400-156544000	Flanking Active TSS	Osteobl	bone
39	chr3:156543400-156544200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr3:156543400-156544200	Active TSS	Fetal Muscle Trunk	muscle
41	chr3:156543400-156544600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:156543400-156544600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:156543400-156544600	Active TSS	Brain Germinal Matrix	brain
44	chr3:156543400-156544600	Active TSS	Brain Substantia Nigra	brain
45	chr3:156543400-156544600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr3:156543400-156544800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
47	chr3:156543400-156544800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
48	chr3:156543400-156544800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:156543400-156544800	Active TSS	Colon Smooth Muscle	Colon
50	chr3:156543400-156545000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell

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