Variant report

Variant	rs1550930
Chromosome Location	chr3:79067965-79067966
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:194)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:194 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:79067920-79068070	HA-sp	spinal cord:	n/a	n/a
2	E2F4	chr3:79067850-79068222	MCF10A-Er-Src	breast:	n/a	chr3:79067996-79068006 chr3:79068100-79068110 chr3:79068005-79068015 chr3:79068002-79068012
3	CTCF	chr3:79067820-79067970	HBMEC	blood vessel:	n/a	n/a
4	TAF1	chr3:79067952-79068958	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr3:79066685-79068055	PFSK-1	brain:	n/a	n/a
6	CTCF	chr3:79067900-79068050	MCF-7	breast:	n/a	n/a
7	CTCF	chr3:79067920-79068070	AG04449	skin:	n/a	n/a
8	CTCF	chr3:79067920-79068210	HA-sp	spinal cord:	n/a	n/a
9	POLR2A	chr3:79067917-79068880	MCF-7	breast:	n/a	n/a
10	POLR2A	chr3:79067799-79068903	ProgFib	skin:	n/a	n/a
11	TBP	chr3:79067640-79069061	H1-hESC	embryonic stem cell:	n/a	n/a
12	MXI1	chr3:79066522-79069115	Hela-S3	cervix:	n/a	n/a
13	MYC	chr3:79067880-79068648	MCF-7	breast:	n/a	n/a
14	CTCF	chr3:79067869-79068080	MCF-7	breast:	n/a	n/a
15	NFIC	chr3:79067680-79068282	ECC-1	luminal epithelium:	n/a	n/a
16	HEY1	chr3:79067851-79068912	HepG2	liver:	n/a	chr3:79068000-79068015 chr3:79067999-79068014
17	CTCF	chr3:79067860-79068010	BJ	skin:	n/a	n/a
18	CTCF	chr3:79067903-79068067	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAX	chr3:79067019-79069052	Hela-S3	cervix:	n/a	n/a
20	SIN3AK20	chr3:79067780-79069074	MCF-7	breast:	n/a	n/a
21	POLR2A	chr3:79066998-79068961	Hela-S3	cervix:	n/a	n/a
22	TBP	chr3:79067683-79068071	Hela-S3	cervix:	n/a	n/a
23	CTCF	chr3:79067900-79068050	HEEpiC	esophagus:	n/a	n/a
24	POLR2A	chr3:79067873-79069199	HEK293	kidney:	n/a	n/a
25	CTCF	chr3:79067834-79068129	H1-hESC	embryonic stem cell:	n/a	n/a
26	MAX	chr3:79067744-79068248	MCF-7	breast:	n/a	n/a
27	RAD21	chr3:79067821-79068206	H1-hESC	embryonic stem cell:	n/a	chr3:79068093-79068107
28	RAD21	chr3:79067783-79068153	HepG2	liver:	n/a	chr3:79068093-79068107
29	BACH1	chr3:79067837-79069031	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr3:79067820-79067970	GM12865	blood:	n/a	n/a
31	CTCF	chr3:79067886-79068038	Gliobla	brain:	n/a	n/a
32	CTCF	chr3:79067909-79068046	GM12891	blood:	n/a	n/a
33	POLR2A	chr3:79067811-79068903	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr3:79067873-79068890	Gliobla	brain:	n/a	n/a
35	CTCF	chr3:79067900-79068050	HPAF	blood vessel:	n/a	n/a
36	CTBP2	chr3:79067762-79069050	H1-hESC	embryonic stem cell:	n/a	n/a
37	MAX	chr3:79067903-79069024	HepG2	liver:	n/a	n/a
38	MAX	chr3:79067724-79069138	HepG2	liver:	n/a	n/a
39	RFX5	chr3:79067942-79068159	HepG2	liver:	n/a	n/a
40	POLR2A	chr3:79067909-79068845	MCF-7	breast:	n/a	n/a
41	CTCF	chr3:79067900-79068050	HAc	cerebellar:	n/a	n/a
42	CTCF	chr3:79067880-79068030	HepG2	liver:	n/a	n/a
43	CTCF	chr3:79067920-79068070	GM06990	blood:	n/a	n/a
44	EP300	chr3:79067703-79069114	ECC-1	luminal epithelium:	n/a	chr3:79068006-79068015 chr3:79068003-79068012 chr3:79068101-79068110 chr3:79067975-79067991 chr3:79068534-79068550 chr3:79068159-79068172
45	TCF7L2	chr3:79066457-79069070	Hela-S3	cervix:	n/a	n/a
46	CTCF	chr3:79067860-79068010	A549	lung:	n/a	n/a
47	CTCF	chr3:79067900-79068050	AG09319	gingival:	n/a	n/a
48	CTCF	chr3:79067900-79068050	HRPEpiC	eye:	n/a	n/a
49	CTCF	chr3:79067826-79068108	IMR90	lung:	n/a	n/a
50	POLR2A	chr3:79067843-79068268	A549	lung:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:79067920-79067970	GM12892	blood:	n/a
2	chr3:79067920-79067970	AoSMC	blood vessel:	n/a
3	chr3:79067920-79067970	HL-60	blood:	n/a
4	chr3:79067920-79067970	HRE	kidney:	n/a
5	chr3:79067920-79067970	SK-N-MC	brain:	n/a
6	chr3:79067920-79067970	HNPCEpiC	eye:	n/a
7	chr3:79067920-79067970	PrEC	prostate:	n/a
8	chr3:79067920-79067970	HCT-116	colon:	n/a
9	chr3:79067920-79067970	HRPEpiC	eye:	n/a
10	chr3:79067920-79067970	AG10803	skin:	n/a
11	chr3:79067920-79067970	HUVEC	blood vessel:	n/a
12	chr3:79067920-79067970	AG04450	lung:	fetal
13	chr3:79067920-79067970	GM12891	blood:	n/a
14	chr3:79067920-79067970	LNCaP	prostate:	n/a
15	chr3:79067920-79067970	HCF	heart:	n/a
16	chr3:79067920-79067970	PANC-1	pancreas:	n/a
17	chr3:79067920-79067970	AG04449	skin:	fetal
18	chr3:79067920-79067970	HIPEpiC	eye:	n/a
19	chr3:79067920-79067970	HPAEpiC	pulmonary alveolar:	n/a
20	chr3:79067920-79067970	HepG2	liver:	n/a
21	chr3:79067920-79067970	GM19239	blood:	n/a
22	chr3:79067920-79067970	MCF10A-Er-Src	breast:	n/a
23	chr3:79067920-79067970	NHDF-neo	bronchial:	n/a
24	chr3:79067920-79067970	HRCEpiC	kidney:	n/a
25	chr3:79067920-79067970	T-47D	breast:	n/a
26	chr3:79067920-79067970	Hela-S3	cervix:	n/a
27	chr3:79067920-79067970	Hepatocyte	liver:	n/a
28	chr3:79067920-79067970	HCPEpiC	choroid plexus:	n/a
29	chr3:79067920-79067970	A549	lung:	n/a
30	chr3:79067920-79067970	NB4	blood:	n/a
31	chr3:79067920-79067970	SAEC	small airway:	n/a
32	chr3:79067920-79067970	RPTEC	kidney:	n/a
33	chr3:79067920-79067970	GM06990	blood:	n/a
34	chr3:79067920-79067970	IMR90	lung:	fetal
35	chr3:79067920-79067970	HCM	heart:	n/a
36	chr3:79067920-79067970	BJ	skin:	n/a
37	chr3:79067920-79067970	GM12878	blood:	n/a
38	chr3:79067920-79067970	HMEC	breast:	n/a
39	chr3:79067920-79067970	ovcar-3	ovarian:	n/a
40	chr3:79067920-79067970	ProgFib	skin:	n/a
41	chr3:79067920-79067970	ECC-1	luminal epithelium:	n/a
42	chr3:79067920-79067970	PFSK-1	brain:	n/a
43	chr3:79067920-79067970	Jurkat	blood:	n/a
44	chr3:79067920-79067970	NHBE	bronchial:	n/a
45	chr3:79067920-79067970	SK-N-SH	brain:	n/a
46	chr3:79067920-79067970	CMK	blood:	n/a
47	chr3:79067920-79067970	NT2-D1	testis:	n/a
48	chr3:79067920-79067970	NH-A	brain:	n/a
49	chr3:79067920-79067970	K562	blood:	n/a
50	chr3:79067920-79067970	BE2_C	brain:	n/a

No data

Variant related genes	Relation type
ROBO1	TF binding region
ROBO1	CpG island

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12495750	1.00[CHD][hapmap]
rs13096526	1.00[CHD][hapmap];1.00[GIH][hapmap]
rs1349022	1.00[ASW][hapmap];1.00[CHD][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs1374881	1.00[EUR][1000 genomes]
rs1374882	1.00[YRI][hapmap]
rs1374883	1.00[CHD][hapmap]
rs1550928	1.00[EUR][1000 genomes]
rs1550929	0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs2121802	1.00[EUR][1000 genomes]
rs4680920	0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs6548603	1.00[CHD][hapmap]
rs6795076	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][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	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv834744	chr3:78911545-79076470	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834745	chr3:79055426-79227937	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:79062600-79069000	Active TSS	Fetal Brain Female	brain
2	chr3:79063600-79069000	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr3:79064200-79069000	Active TSS	Brain Anterior Caudate	brain
4	chr3:79064200-79069000	Active TSS	NHLF	lung
5	chr3:79064200-79069400	Active TSS	H1 Cell Line	embryonic stem cell
6	chr3:79064400-79069000	Active TSS	Right Atrium	heart
7	chr3:79064400-79069200	Active TSS	Stomach Smooth Muscle	stomach
8	chr3:79064600-79069000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:79064600-79069000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:79064600-79069000	Active TSS	Brain Angular Gyrus	brain
11	chr3:79064600-79069000	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr3:79064600-79069400	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr3:79064800-79068800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:79064800-79069000	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr3:79064800-79069000	Active TSS	Brain Substantia Nigra	brain
16	chr3:79065000-79069000	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr3:79065200-79069000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:79065200-79069200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
19	chr3:79065400-79068200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:79065400-79068800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
21	chr3:79065400-79069000	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr3:79065400-79069000	Active TSS	Brain Hippocampus Middle	brain
23	chr3:79065400-79069000	Active TSS	Fetal Lung	lung
24	chr3:79065400-79069000	Active TSS	Fetal Stomach	stomach
25	chr3:79065400-79069000	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr3:79065400-79069000	Active TSS	A549	lung
27	chr3:79065400-79069200	Active TSS	GM12878-XiMat	blood
28	chr3:79065600-79068800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr3:79065600-79069000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:79065600-79069000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:79065600-79069000	Active TSS	Fetal Kidney	kidney
32	chr3:79065600-79069000	Active TSS	Ovary	ovary
33	chr3:79065600-79069000	Active TSS	NHDF-Ad	bronchial
34	chr3:79065800-79068000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:79065800-79069000	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr3:79065800-79069000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr3:79065800-79069000	Active TSS	Psoas Muscle	Psoas
38	chr3:79065800-79069000	Active TSS	HSMM	muscle
39	chr3:79065800-79069200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:79066000-79068800	Active TSS	Hela-S3	cervix
41	chr3:79066000-79069000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr3:79066000-79069000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:79066000-79069000	Active TSS	H9 Cell Line	embryonic stem cell
44	chr3:79066000-79069000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:79066000-79069000	Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr3:79066000-79069000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr3:79066000-79069000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:79066000-79069000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:79066000-79069000	Active TSS	Muscle Satellite Cultured Cells	--
50	chr3:79066000-79069000	Active TSS	Colonic Mucosa	Colon

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