Variant report

Variant	rs3755557
Chromosome Location	chr3:119814957-119814958
allele	A/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	POU2F2	chr3:119813538-119815083	GM12878	blood:	n/a	n/a
2	ATF2	chr3:119812342-119815042	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:119812666-119815257	HEK293	kidney:	n/a	n/a
4	CBX3	chr3:119813729-119815009	K562	blood:	n/a	n/a
5	REST	chr3:119813796-119815047	HL-60	blood:	n/a	chr3:119813925-119813932
6	POLR2A	chr3:119813808-119815061	GM12878	blood:	n/a	n/a
7	JUND	chr3:119813801-119815007	H1-hESC	embryonic stem cell:	n/a	chr3:119814052-119814061 chr3:119813932-119813941
8	TCF12	chr3:119812183-119815169	A549	lung:	n/a	n/a
9	KAP1	chr3:119813660-119815055	HEK293	kidney:	n/a	n/a
10	POLR2A	chr3:119812597-119815213	Raji	blood:	n/a	n/a
11	POLR2A	chr3:119812621-119815043	GM19193	blood:	n/a	n/a
12	POLR2A	chr3:119811683-119815493	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr3:119812046-119815097	PBDE	blood:	n/a	n/a
14	MAZ	chr3:119811823-119815143	GM12878	blood:	n/a	chr3:119812593-119812612
15	POLR2A	chr3:119812529-119815276	HCT-116	colon:	n/a	n/a
16	POLR2A	chr3:119813547-119815409	ECC-1	luminal epithelium:	n/a	n/a
17	RFX5	chr3:119812846-119815112	GM12878	blood:	n/a	chr3:119814006-119814015 chr3:119813079-119813094 chr3:119813666-119813674 chr3:119813487-119813496 chr3:119813036-119813052 chr3:119813676-119813685 chr3:119813933-119813942
18	POLR2A	chr3:119812680-119815142	K562	blood:	n/a	n/a
19	STAT5A	chr3:119813830-119815101	GM12878	blood:	n/a	chr3:119813973-119813985
20	SIN3AK20	chr3:119813670-119814972	MCF-7	breast:	n/a	n/a
21	TBP	chr3:119813219-119815027	HepG2	liver:	n/a	n/a
22	ELK4	chr3:119814447-119815267	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr3:119813736-119815400	GM12892	blood:	n/a	n/a
24	TAF1	chr3:119812497-119814966	ECC-1	luminal epithelium:	n/a	n/a
25	YY1	chr3:119812391-119815069	SK-N-SH	brain:	n/a	chr3:119813179-119813193 chr3:119813997-119814006 chr3:119813401-119813410 chr3:119814000-119814009 chr3:119813302-119813316 chr3:119813177-119813188 chr3:119813307-119813318 chr3:119813399-119813413 chr3:119812933-119812947
26	HEY1	chr3:119812557-119814979	HepG2	liver:	n/a	chr3:119813391-119813406 chr3:119813098-119813113
27	EP300	chr3:119813198-119814978	GM12878	blood:	n/a	chr3:119814070-119814086 chr3:119813404-119813413 chr3:119813999-119814008 chr3:119814849-119814863
28	MYBL2	chr3:119813118-119815086	HepG2	liver:	n/a	n/a
29	TAF1	chr3:119812603-119814977	MCF-7	breast:	n/a	n/a
30	GATA3	chr3:119814334-119815148	T-47D	breast:	n/a	chr3:119814838-119814849 chr3:119814831-119814852
31	MAX	chr3:119812526-119815100	MCF-7	breast:	n/a	chr3:119812593-119812612
32	POLR2A	chr3:119812204-119815123	K562	blood:	n/a	n/a
33	POLR2A	chr3:119811867-119815267	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr3:119812509-119815211	ProgFib	skin:	n/a	n/a
35	POLR2A	chr3:119813529-119815142	HL-60	blood:	n/a	n/a
36	POLR2A	chr3:119812644-119815147	K562	blood:	n/a	n/a
37	POLR2A	chr3:119812629-119815237	H1-hESC	embryonic stem cell:	n/a	n/a
38	TEAD4	chr3:119813845-119814965	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr3:119812636-119815239	GM12878	blood:	n/a	n/a
40	POLR2A	chr3:119812648-119815198	GM18505	blood:	n/a	n/a
41	RELA	chr3:119813287-119814971	GM18526	blood:	n/a	n/a
42	POLR2A	chr3:119812501-119815293	HUVEC	blood vessel:	n/a	n/a
43	POLR2A	chr3:119812737-119814999	K562	blood:	n/a	n/a
44	POLR2A	chr3:119812649-119815005	GM15510	blood:	n/a	n/a
45	POLR2A	chr3:119813573-119815281	GM12891	blood:	n/a	n/a
46	MAX	chr3:119811344-119815256	Hela-S3	cervix:	n/a	chr3:119812593-119812612
47	POLR2A	chr3:119813748-119815274	GM12891	blood:	n/a	n/a
48	POLR2A	chr3:119812622-119815230	GM12891	blood:	n/a	n/a
49	WRNIP1	chr3:119813615-119814989	GM12878	blood:	n/a	n/a
50	POLR2A	chr3:119812122-119815261	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:119810967..119815661-chr3:120066752..120069801,5	K562	blood:
2	chr3:119812158..119817554-chr3:119829250..119832588,6	K562	blood:
3	chr3:119181413..119183027-chr3:119814257..119816285,2	MCF-7	breast:
4	chr3:119812996..119815585-chrX:153772819..153775165,2	MCF-7	breast:
5	chr1:108742013..108742800-chr3:119814585..119815177,2	Hela-S3	cervix:
6	chr3:119814526..119816268-chr3:119818029..119819760,2	K562	blood:
7	chr3:119758303..119760523-chr3:119813063..119815758,2	K562	blood:
8	chr3:119812621..119817617-chr3:119824950..119830930,7	K562	blood:
9	chr3:119812799..119816595-chr3:119829619..119835566,15	MCF-7	breast:
10	chr3:119811895..119815177-chr3:120067061..120069801,4	K562	blood:
11	chr3:119408612..119410162-chr3:119814493..119816849,2	K562	blood:
12	chr3:119814026..119816300-chr3:120067212..120070079,2	MCF-7	breast:
13	chr3:119394727..119396286-chr3:119814089..119815777,2	K562	blood:
14	chr3:119813314..119815193-chr3:120066557..120069483,2	MCF-7	breast:
15	chr17:56708450..56710386-chr3:119813932..119815937,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NR1I2-1	chr3:119814171-119815030	XLOC_002779
2	lnc-NR1I2-1	chr3:119814901-119815030	XLOC_002779
3	lnc-NR1I2-1	chr3:119814926-119815030	XLOC_002779
4	lnc-NR1I2-1	chr3:119814913-119815030	XLOC_002779
5	lnc-NR1I2-1	chr3:119813266-119819259	NONHSAT091417
6	lnc-NR1I2-1	chr3:119814677-119815030	NONHSAT091425
7	lnc-NR1I2-1	chr3:119814171-119815030	XLOC_002779
8	lnc-NR1I2-1	chr3:119814913-119815030	ENSG00000242622

Variant related genes	Relation type
GSK3B	TF binding region
ENSG00000163428	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000260879	Chromatin interaction
ENSG00000073009	Chromatin interaction
ENSG00000244308	Chromatin interaction
ENSG00000176142	Chromatin interaction
ENSG00000160211	Chromatin interaction
ENSG00000240661	Chromatin interaction
ENSG00000241546	Chromatin interaction
ENSG00000138495	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11925868	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11925899	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11925952	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16830720	0.87[ASN][1000 genomes]
rs17811013	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs17811061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58959678	0.80[ASN][1000 genomes]
rs62266287	0.83[ASN][1000 genomes]
rs73177909	0.95[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv3964	chr3:119786623-119831698	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv829697	chr3:119802856-119918435	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	59 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	chr3:119808000-119816400	Active TSS	Fetal Brain Female	brain
2	chr3:119808200-119815000	Active TSS	HMEC	breast
3	chr3:119808400-119815600	Active TSS	GM12878-XiMat	blood
4	chr3:119808800-119815000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:119808800-119815600	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr3:119809000-119815000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:119809000-119816200	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr3:119809200-119815000	Active TSS	HSMMtube	muscle
9	chr3:119809200-119815400	Active TSS	Psoas Muscle	Psoas
10	chr3:119809200-119815400	Active TSS	Right Ventricle	heart
11	chr3:119809200-119815600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:119809200-119815600	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr3:119809200-119815800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:119809200-119816000	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr3:119809200-119816200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:119809400-119815000	Active TSS	Fetal Thymus	thymus
17	chr3:119809400-119815000	Active TSS	Ovary	ovary
18	chr3:119809400-119815200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:119809400-119815400	Active TSS	Aorta	Aorta
20	chr3:119809400-119815600	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr3:119809400-119815800	Active TSS	HSMM	muscle
22	chr3:119809400-119816000	Active TSS	H1 Cell Line	embryonic stem cell
23	chr3:119809600-119815000	Active TSS	Fetal Intestine Large	intestine
24	chr3:119809600-119815000	Active TSS	Fetal Lung	lung
25	chr3:119809600-119815000	Active TSS	Fetal Muscle Leg	muscle
26	chr3:119809600-119815200	Active TSS	Left Ventricle	heart
27	chr3:119809600-119815400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr3:119809600-119815600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:119809600-119815800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:119809600-119815800	Active TSS	NHLF	lung
31	chr3:119809600-119816000	Active TSS	H9 Cell Line	embryonic stem cell
32	chr3:119809800-119815000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:119809800-119815000	Active TSS	Fetal Intestine Small	intestine
34	chr3:119809800-119815800	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr3:119809800-119815800	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr3:119810000-119815000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:119810000-119815000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:119810000-119815000	Active TSS	Colon Smooth Muscle	Colon
39	chr3:119810000-119815000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr3:119810000-119815000	Active TSS	Thymus	Thymus
41	chr3:119810000-119815000	Active TSS	NHDF-Ad	bronchial
42	chr3:119810000-119815200	Active TSS	Brain Substantia Nigra	brain
43	chr3:119810000-119815200	Active TSS	A549	lung
44	chr3:119810000-119815400	Active TSS	Brain Germinal Matrix	brain
45	chr3:119810000-119815600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:119810000-119815800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:119810000-119816200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:119810000-119816200	Active TSS	K562	blood
49	chr3:119810200-119815000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:119810200-119816000	Active TSS	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links