Variant report

Variant	rs2018246
Chromosome Location	chr3:150481937-150481938
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:371)
CpG islands
(count:61)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:371 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:150476883-150483109	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:150480310-150481986	HCT-116	colon:	n/a	n/a
3	CTCF	chr3:150481800-150481950	WERI-Rb-1	eye:	n/a	n/a
4	HDAC2	chr3:150480754-150481993	HepG2	liver:	n/a	n/a
5	YY1	chr3:150481697-150481972	K562	blood:	n/a	n/a
6	ATF2	chr3:150480894-150482108	GM12878	blood:	n/a	chr3:150480943-150480957
7	MXI1	chr3:150479220-150482056	GM12878	blood:	n/a	n/a
8	CTCF	chr3:150481800-150481950	Caco-2	colon:	n/a	n/a
9	CREB1	chr3:150480742-150482015	K562	blood:	n/a	n/a
10	CTBP2	chr3:150479678-150481976	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr3:150481750-150481970	SK-N-SH_RA	brain:	n/a	n/a
12	EP300	chr3:150480806-150482021	HepG2	liver:	n/a	n/a
13	POLR2A	chr3:150479212-150482050	MCF-7	breast:	n/a	n/a
14	POLR2A	chr3:150479559-150482054	HepG2	liver:	n/a	n/a
15	NR2F2	chr3:150480551-150482176	MCF-7	breast:	n/a	n/a
16	POLR2A	chr3:150481903-150481992	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:150479714-150483006	GM18505	blood:	n/a	n/a
18	CTCF	chr3:150481698-150481979	Gliobla	brain:	n/a	n/a
19	POLR2A	chr3:150479676-150482089	GM19099	blood:	n/a	n/a
20	POLR2A	chr3:150479339-150482294	Hela-S3	cervix:	n/a	n/a
21	CTCF	chr3:150481820-150481970	HRPEpiC	eye:	n/a	n/a
22	SIN3AK20	chr3:150480689-150482186	MCF-7	breast:	n/a	n/a
23	GATA3	chr3:150480575-150482134	MCF-7	breast:	n/a	n/a
24	POLR2A	chr3:150480590-150482029	H1-neurons	neurons:	n/a	n/a
25	MAX	chr3:150480555-150482120	HepG2	liver:	n/a	n/a
26	MAX	chr3:150480762-150482061	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr3:150480098-150482035	HL-60	blood:	n/a	n/a
28	CTCF	chr3:150481820-150481970	HMF	breast:	n/a	n/a
29	CTCF	chr3:150481800-150481950	AG04450	lung:	n/a	n/a
30	ZNF143	chr3:150480751-150482001	Hela-S3	cervix:	n/a	chr3:150481561-150481571 chr3:150480758-150480768
31	MAX	chr3:150480493-150482029	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr3:150481765-150481963	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr3:150479623-150483088	GM19193	blood:	n/a	n/a
34	POLR2A	chr3:150480625-150482081	PANC-1	pancreas:	n/a	n/a
35	RCOR1	chr3:150480802-150482014	HepG2	liver:	n/a	n/a
36	RAD21	chr3:150481408-150482048	HepG2	liver:	n/a	chr3:150481507-150481519
37	MAX	chr3:150479554-150482049	Hela-S3	cervix:	n/a	n/a
38	BCLAF1	chr3:150480702-150482136	GM12878	blood:	n/a	chr3:150480817-150480830
39	CTCF	chr3:150481655-150481978	Fibrobl	skin:	n/a	n/a
40	CTCF	chr3:150479370-150482380	A549	lung:	n/a	chr3:150480869-150480882
41	TBL1XR1	chr3:150480991-150482024	K562	blood:	n/a	n/a
42	POLR2A	chr3:150478964-150483373	HepG2	liver:	n/a	n/a
43	GATA1	chr3:150480755-150481995	PBDE	blood:	n/a	n/a
44	MYC	chr3:150481716-150481983	HepG2	liver:	n/a	n/a
45	CTCF	chr3:150481800-150481950	HEK293	kidney:	n/a	n/a
46	CTCF	chr3:150481629-150482051	K562	blood:	n/a	n/a
47	POLR2A	chr3:150480547-150482133	HUVEC	blood vessel:	n/a	n/a
48	CTCF	chr3:150481666-150481988	LNCaP	prostate:	n/a	n/a
49	CTCF	chr3:150481678-150481977	GM19240	blood:	n/a	n/a
50	MAZ	chr3:150480815-150481991	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:150481914-150481964	AG09309	skin:	n/a
2	chr3:150481914-150481964	HEK293	kidney:	embryo
3	chr3:150481914-150481964	PFSK-1	brain:	n/a
4	chr3:150481914-150481964	HNPCEpiC	eye:	n/a
5	chr3:150481914-150481964	NHBE	bronchial:	n/a
6	chr3:150481914-150481964	PrEC	prostate:	n/a
7	chr3:150481914-150481964	HRE	kidney:	n/a
8	chr3:150481914-150481964	Caco-2	colon:	n/a
9	chr3:150481914-150481964	HRCEpiC	kidney:	n/a
10	chr3:150481914-150481964	SAEC	small airway:	n/a
11	chr3:150481914-150481964	HRPEpiC	eye:	n/a
12	chr3:150481914-150481964	SKMC	muscle:	n/a
13	chr3:150481914-150481964	ProgFib	skin:	n/a
14	chr3:150481914-150481964	GM19239	blood:	n/a
15	chr3:150481914-150481964	PANC-1	pancreas:	n/a
16	chr3:150481914-150481964	IMR90	lung:	fetal
17	chr3:150481914-150481964	CMK	blood:	n/a
18	chr3:150481914-150481964	SK-N-SH	brain:	n/a
19	chr3:150481914-150481964	U87	brain:	n/a
20	chr3:150481914-150481964	NB4	blood:	n/a
21	chr3:150481914-150481964	HUVEC	blood vessel:	n/a
22	chr3:150481914-150481964	AG10803	skin:	n/a
23	chr3:150481914-150481964	ECC-1	luminal epithelium:	n/a
24	chr3:150481914-150481964	GM06990	blood:	n/a
25	chr3:150481914-150481964	ovcar-3	ovarian:	n/a
26	chr3:150481914-150481964	MCF-7	breast:	n/a
27	chr3:150481914-150481964	SK-N-SH_RA	brain:	n/a
28	chr3:150481914-150481964	A549	lung:	n/a
29	chr3:150481914-150481964	HIPEpiC	eye:	n/a
30	chr3:150481914-150481964	HCT-116	colon:	n/a
31	chr3:150481914-150481964	Jurkat	blood:	n/a
32	chr3:150481914-150481964	T-47D	breast:	n/a
33	chr3:150481914-150481964	HCM	heart:	n/a
34	chr3:150481914-150481964	AG04449	skin:	fetal
35	chr3:150481914-150481964	NH-A	brain:	n/a
36	chr3:150481914-150481964	GM12892	blood:	n/a
37	chr3:150481914-150481964	NHDF-neo	bronchial:	n/a
38	chr3:150481914-150481964	HMEC	breast:	n/a
39	chr3:150481914-150481964	K562	blood:	n/a
40	chr3:150481914-150481964	HAEpiC	amniotic membrane:	n/a
41	chr3:150481914-150481964	BJ	skin:	n/a
42	chr3:150481914-150481964	LNCaP	prostate:	n/a
43	chr3:150481914-150481964	HEEpiC	esophagus:	n/a
44	chr3:150481914-150481964	H1-hESC	embryonic stem cell:	embryo
45	chr3:150481914-150481964	HepG2	liver:	n/a
46	chr3:150481914-150481964	Hela-S3	cervix:	n/a
47	chr3:150481914-150481964	Hepatocyte	liver:	n/a
48	chr3:150481914-150481964	BE2_C	brain:	n/a
49	chr3:150481914-150481964	GM12891	blood:	n/a
50	chr3:150481914-150481964	MCF10A-Er-Src	breast:	n/a

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:150318777..150323048-chr3:150479715..150482584,4	K562	blood:
2	chr20:55753885..55754468-chr3:150481272..150482133,2	MCF-7	breast:
3	chr3:150481412..150481942-chr3:150547893..150548575,2	MCF-7	breast:
4	chr3:150438835..150439759-chr3:150481383..150482353,4	MCF-7	breast:
5	chr22:37956970..37957729-chr3:150481295..150482246,2	Hela-S3	cervix:
6	chr3:150399970..150401503-chr3:150480432..150482241,2	K562	blood:
7	chr17:79825898..79826714-chr3:150481279..150482274,2	Hela-S3	cervix:
8	chr20:30194436..30195217-chr3:150481124..150482095,2	Hela-S3	cervix:
9	chr3:150319354..150323687-chr3:150477863..150484487,11	MCF-7	breast:
10	chr3:150421205..150424923-chr3:150480120..150484463,5	MCF-7	breast:
11	chr3:150261800..150265866-chr3:150477764..150484308,7	MCF-7	breast:
12	chr12:107364565..107365547-chr3:150481458..150482307,2	Hela-S3	cervix:
13	chr3:150125257..150128558-chr3:150478258..150482422,4	K562	blood:
14	chr3:150318641..150323079-chr3:150479217..150482794,6	MCF-7	breast:
15	chr3:150433681..150449199-chr3:150473254..150487048,35	MCF-7	breast:

No data

Variant related genes	Relation type
SIAH2	TF binding region
SIAH2	CpG island
ENSG00000240137	Chromatin interaction
ENSG00000141522	Chromatin interaction
ENSG00000144895	Chromatin interaction
ENSG00000120742	Chromatin interaction
ENSG00000198843	Chromatin interaction
ENSG00000244668	Chromatin interaction
ENSG00000196428	Chromatin interaction
ENSG00000151135	Chromatin interaction
ENSG00000163645	Chromatin interaction
ENSG00000264395	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1444197	1.00[CEU][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs1533711	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16862837	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16862842	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1814463	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1814464	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1838337	0.81[EUR][1000 genomes]
rs1879420	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs1879421	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1879422	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1915365	0.81[EUR][1000 genomes]
rs1991781	0.84[ASN][1000 genomes]
rs2014279	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2116684	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs2116685	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2166061	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2869479	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34348847	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34771595	0.87[EUR][1000 genomes]
rs3851356	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41372346	1.00[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs41454348	1.00[CEU][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap]
rs481236	0.80[ASN][1000 genomes]
rs55899470	0.84[ASN][1000 genomes]
rs57275328	0.82[ASN][1000 genomes]
rs57278175	0.87[EUR][1000 genomes]
rs57824095	0.84[ASN][1000 genomes]
rs57869178	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58403524	0.81[EUR][1000 genomes]
rs58418105	0.83[ASN][1000 genomes]
rs60259684	1.00[EUR][1000 genomes]
rs60523415	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6440696	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6440697	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs6440698	0.88[EUR][1000 genomes]
rs6769917	1.00[EUR][1000 genomes]
rs6777178	1.00[EUR][1000 genomes]
rs6788895	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6789306	1.00[CEU][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs6795396	0.87[EUR][1000 genomes]
rs6803830	0.81[EUR][1000 genomes]
rs6805481	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6806197	0.87[EUR][1000 genomes]
rs71764080	0.81[EUR][1000 genomes]
rs72993403	0.81[EUR][1000 genomes]
rs73003787	0.87[EUR][1000 genomes]
rs73003792	1.00[EUR][1000 genomes]
rs73005814	0.82[EUR][1000 genomes]
rs73006999	0.84[ASN][1000 genomes]
rs73008903	0.84[ASN][1000 genomes]
rs73008905	0.84[ASN][1000 genomes]
rs73008907	0.84[ASN][1000 genomes]
rs73010930	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73010941	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73010947	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73010956	1.00[EUR][1000 genomes]
rs73010964	1.00[EUR][1000 genomes]
rs73010965	1.00[EUR][1000 genomes]
rs73010967	0.81[EUR][1000 genomes]
rs73869297	0.87[EUR][1000 genomes]
rs7615125	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs7615292	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs7617507	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7628481	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7628776	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7636866	1.00[CEU][hapmap];0.84[JPT][hapmap];0.82[ASN][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	nsv532662	chr3:150180747-150633414	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1820145	chr3:150478018-150487945	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	esv3420624	chr3:150478562-150482960	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150478000-150482000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr3:150478000-150482200	Active TSS	Thymus	Thymus
3	chr3:150478200-150482000	Active TSS	Ovary	ovary
4	chr3:150478200-150482200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:150478200-150482200	Active TSS	Right Ventricle	heart
6	chr3:150478200-150482200	Active TSS	NHDF-Ad	bronchial
7	chr3:150478200-150482400	Active TSS	Placenta	Placenta
8	chr3:150478200-150482400	Active TSS	GM12878-XiMat	blood
9	chr3:150478400-150482000	Active TSS	HSMM	muscle
10	chr3:150478400-150482200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:150478400-150482200	Active TSS	HSMMtube	muscle
12	chr3:150478400-150482600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:150478600-150482000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:150478600-150482000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:150478600-150482200	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr3:150478600-150482200	Active TSS	Aorta	Aorta
17	chr3:150478600-150482400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:150478600-150482600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:150478800-150482000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:150478800-150482000	Active TSS	Sigmoid Colon	Sigmoid Colon
21	chr3:150478800-150482000	Active TSS	K562	blood
22	chr3:150478800-150482200	Active TSS	Psoas Muscle	Psoas
23	chr3:150478800-150482200	Active TSS	NHLF	lung
24	chr3:150479000-150482000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:150479000-150482200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
26	chr3:150479000-150482200	Active TSS	Brain Germinal Matrix	brain
27	chr3:150479200-150482000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr3:150479200-150482000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:150479200-150482000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr3:150479200-150482200	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr3:150479200-150482200	Active TSS	Fetal Muscle Leg	muscle
32	chr3:150479200-150482200	Active TSS	A549	lung
33	chr3:150479200-150482400	Active TSS	Fetal Intestine Large	intestine
34	chr3:150479400-150482000	Active TSS	H9 Cell Line	embryonic stem cell
35	chr3:150479400-150482000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
36	chr3:150479400-150482000	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr3:150479400-150482000	Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr3:150479400-150482000	Active TSS	Brain Cingulate Gyrus	brain
39	chr3:150479400-150482000	Active TSS	Fetal Kidney	kidney
40	chr3:150479400-150482000	Active TSS	Left Ventricle	heart
41	chr3:150479400-150482000	Active TSS	Placenta Amnion	Placenta Amnion
42	chr3:150479400-150482000	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr3:150479400-150482000	Active TSS	Small Intestine	intestine
44	chr3:150479400-150482000	Active TSS	Osteobl	bone
45	chr3:150479400-150482200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:150479400-150482200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr3:150479400-150482200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:150479400-150482200	Active TSS	Liver	Liver
49	chr3:150479400-150482200	Active TSS	Brain Substantia Nigra	brain
50	chr3:150479400-150482200	Active TSS	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links