Variant report

Variant	rs2172315
Chromosome Location	chr3:111853298-111853299
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:48)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:48 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:111850784-111853964	GM12891	blood:	n/a	n/a
2	RUNX3	chr3:111850883-111854136	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:111846191-111854054	GM12892	blood:	n/a	n/a
4	POU2F2	chr3:111852468-111853376	GM12878	blood:	n/a	n/a
5	EBF1	chr3:111851012-111856368	GM12878	blood:	n/a	chr3:111852245-111852256
6	RUNX3	chr3:111850936-111853979	GM12878	blood:	n/a	n/a
7	EP300	chr3:111851070-111854042	GM12878	blood:	n/a	chr3:111851867-111851881 chr3:111851873-111851887 chr3:111852008-111852017
8	EP300	chr3:111853207-111854205	SK-N-SH	brain:	n/a	n/a
9	GATA1	chr3:111853255-111854130	PBDE	blood:	n/a	n/a
10	PML	chr3:111850554-111854266	GM12878	blood:	n/a	chr3:111852106-111852114
11	STAT5A	chr3:111850377-111854015	GM12878	blood:	n/a	chr3:111851865-111851876 chr3:111851072-111851092 chr3:111851295-111851306
12	POLR2A	chr3:111850789-111854058	GM12892	blood:	n/a	n/a
13	POLR2A	chr3:111850717-111854239	GM12892	blood:	n/a	n/a
14	BCLAF1	chr3:111850867-111854010	GM12878	blood:	n/a	chr3:111851873-111851882 chr3:111852251-111852260 chr3:111851984-111851993 chr3:111852131-111852144
15	NFIC	chr3:111853158-111857194	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:111850956-111853341	GM19099	blood:	n/a	n/a
17	TBL1XR1	chr3:111850671-111854123	GM12878	blood:	n/a	n/a
18	BHLHE40	chr3:111853246-111854032	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:111850835-111853668	GM12878	blood:	n/a	n/a
20	POLR2A	chr3:111846299-111854337	Raji	blood:	n/a	n/a
21	NFATC1	chr3:111846108-111854042	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:111852558-111853423	GM12878	blood:	n/a	n/a
23	CHD2	chr3:111850980-111854030	GM12878	blood:	n/a	n/a
24	WRNIP1	chr3:111852545-111853475	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:111850847-111853999	GM12878	blood:	n/a	n/a
26	POLR2A	chr3:111846063-111856284	GM12878	blood:	n/a	n/a
27	POLR2A	chr3:111850803-111853468	GM12891	blood:	n/a	n/a
28	FOXM1	chr3:111850792-111853336	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:111852496-111853708	GM12891	blood:	n/a	n/a
30	FOXM1	chr3:111853219-111854022	GM12878	blood:	n/a	n/a
31	POLR2A	chr3:111850773-111856379	GM12878	blood:	n/a	n/a
32	POLR2A	chr3:111846207-111853952	GM12892	blood:	n/a	n/a
33	POLR2A	chr3:111852611-111853419	GM12878	blood:	n/a	n/a
34	BCLAF1	chr3:111850777-111854285	GM12878	blood:	n/a	chr3:111851873-111851882 chr3:111852251-111852260 chr3:111851984-111851993 chr3:111852131-111852144
35	POLR2A	chr3:111846124-111855250	GM12878	blood:	n/a	n/a
36	POLR2A	chr3:111843489-111856486	GM12878	blood:	n/a	n/a
37	POU2F2	chr3:111850889-111853496	GM12878	blood:	n/a	n/a
38	POLR2A	chr3:111847163-111853431	GM15510	blood:	n/a	n/a
39	ZNF143	chr3:111851731-111853965	GM12878	blood:	n/a	n/a
40	MTA3	chr3:111845901-111857252	GM12878	blood:	n/a	n/a
41	MAX	chr3:111850962-111853387	GM12878	blood:	n/a	chr3:111852319-111852327 chr3:111852129-111852139
42	MTA3	chr3:111846320-111854316	GM12878	blood:	n/a	n/a
43	ATF2	chr3:111853198-111854260	GM12878	blood:	n/a	n/a
44	POLR2A	chr3:111846225-111854392	GM12891	blood:	n/a	n/a
45	NFIC	chr3:111853200-111854139	GM12878	blood:	n/a	n/a
46	POLR2A	chr3:111846166-111854300	GM12892	blood:	n/a	n/a
47	ATF2	chr3:111850206-111854200	GM12878	blood:	n/a	n/a
48	POLR2A	chr3:111846124-111854277	GM18505	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:111853297-111853347	SAEC	small airway:	n/a
2	chr3:111853297-111853347	GM06990	blood:	n/a
3	chr3:111853297-111853347	HEEpiC	esophagus:	n/a
4	chr3:111853297-111853347	HNPCEpiC	eye:	n/a
5	chr3:111853297-111853347	AG04450	lung:	fetal
6	chr3:111853297-111853347	MCF10A-Er-Src	breast:	n/a
7	chr3:111853297-111853347	AG04449	skin:	fetal
8	chr3:111853297-111853347	HRE	kidney:	n/a
9	chr3:111853297-111853347	GM12892	blood:	n/a
10	chr3:111853297-111853347	BJ	skin:	n/a
11	chr3:111853297-111853347	H1-hESC	embryonic stem cell:	embryo
12	chr3:111853297-111853347	CMK	blood:	n/a
13	chr3:111853297-111853347	Caco-2	colon:	n/a
14	chr3:111853297-111853347	NT2-D1	testis:	n/a
15	chr3:111853297-111853347	SK-N-SH	brain:	n/a
16	chr3:111853297-111853347	HCF	heart:	n/a
17	chr3:111853297-111853347	GM12878	blood:	n/a
18	chr3:111853297-111853347	NH-A	brain:	n/a
19	chr3:111853297-111853347	PrEC	prostate:	n/a
20	chr3:111853297-111853347	AG10803	skin:	n/a
21	chr3:111853297-111853347	AoSMC	blood vessel:	n/a
22	chr3:111853297-111853347	RPTEC	kidney:	n/a
23	chr3:111853297-111853347	SK-N-SH_RA	brain:	n/a
24	chr3:111853297-111853347	U87	brain:	n/a
25	chr3:111853297-111853347	HCM	heart:	n/a
26	chr3:111853297-111853347	HepG2	liver:	n/a
27	chr3:111853297-111853347	AG09319	gingival:	n/a
28	chr3:111853297-111853347	ECC-1	luminal epithelium:	n/a
29	chr3:111853297-111853347	HCPEpiC	choroid plexus:	n/a
30	chr3:111853297-111853347	ProgFib	skin:	n/a
31	chr3:111853297-111853347	AG09309	skin:	n/a
32	chr3:111853297-111853347	LNCaP	prostate:	n/a
33	chr3:111853297-111853347	HEK293	kidney:	embryo
34	chr3:111853297-111853347	Jurkat	blood:	n/a
35	chr3:111853297-111853347	HCT-116	colon:	n/a
36	chr3:111853297-111853347	Hela-S3	cervix:	n/a
37	chr3:111853297-111853347	ovcar-3	ovarian:	n/a
38	chr3:111853297-111853347	T-47D	breast:	n/a
39	chr3:111853297-111853347	MCF-7	breast:	n/a
40	chr3:111853297-111853347	NHDF-neo	bronchial:	n/a
41	chr3:111853297-111853347	PANC-1	pancreas:	n/a
42	chr3:111853297-111853347	HIPEpiC	eye:	n/a
43	chr3:111853297-111853347	PFSK-1	brain:	n/a
44	chr3:111853297-111853347	HL-60	blood:	n/a
45	chr3:111853297-111853347	NB4	blood:	n/a
46	chr3:111853297-111853347	IMR90	lung:	fetal
47	chr3:111853297-111853347	GM12891	blood:	n/a
48	chr3:111853297-111853347	SK-N-MC	brain:	n/a
49	chr3:111853297-111853347	BE2_C	brain:	n/a
50	chr3:111853297-111853347	HAEpiC	amniotic membrane:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C3orf52-1	chr3:111852270-111854206	ENSG00000261488.1

No data

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

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11719485	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12634031	0.82[EUR][1000 genomes]
rs13314268	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13314792	0.82[EUR][1000 genomes]
rs1492482	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1492487	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1602671	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2029636	0.82[EUR][1000 genomes]
rs2029637	0.82[EUR][1000 genomes]
rs2046983	0.85[EUR][1000 genomes]
rs2087768	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2131232	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2172314	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2399405	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3929356	0.82[EUR][1000 genomes]
rs4682356	0.80[ASN][1000 genomes]
rs4682365	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs62277462	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6766622	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6767017	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6773161	0.82[EUR][1000 genomes]
rs6784524	0.82[EUR][1000 genomes]
rs6791042	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6805795	0.82[EUR][1000 genomes]
rs6808920	0.82[EUR][1000 genomes]
rs7622733	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9288937	0.83[EUR][1000 genomes]
rs9288938	0.82[EUR][1000 genomes]
rs9821935	0.82[EUR][1000 genomes]
rs9827894	0.82[EUR][1000 genomes]
rs9835431	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9851173	0.84[EUR][1000 genomes]
rs9861756	0.84[EUR][1000 genomes]
rs9871650	0.82[EUR][1000 genomes]

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111834200-111853800	Weak transcription	Fetal Intestine Small	intestine
2	chr3:111840800-111855800	Weak transcription	NH-A	brain
3	chr3:111844800-111855800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:111845600-111855800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:111848200-111857000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:111848400-111853800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:111848400-111854600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:111848400-111854800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:111848400-111855800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:111848400-111856000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:111848400-111856800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:111848800-111853600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:111848800-111854200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:111849000-111854800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:111849200-111855000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:111851600-111854600	Enhancers	Primary hematopoietic stem cells	blood
17	chr3:111851800-111853400	Enhancers	Fetal Muscle Leg	muscle
18	chr3:111852000-111853400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:111852000-111853400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr3:111852000-111853600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr3:111852200-111853600	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr3:111852200-111854200	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr3:111852200-111855000	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr3:111852200-111855200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:111852200-111857000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:111852200-111857600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:111852200-111863400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:111852400-111854600	Enhancers	Primary T cells fromperipheralblood	blood
29	chr3:111852400-111855200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr3:111852400-111856200	Enhancers	Fetal Thymus	thymus
31	chr3:111852400-111856200	Enhancers	Thymus	Thymus
32	chr3:111852400-111856600	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr3:111852400-111856600	Flanking Active TSS	GM12878-XiMat	blood
34	chr3:111852400-111857000	Enhancers	Primary B cells from cord blood	blood
35	chr3:111852400-111857200	Enhancers	Primary B cells from peripheral blood	blood
36	chr3:111852600-111853400	Enhancers	Gastric	stomach
37	chr3:111852600-111853600	Weak transcription	HMEC	breast
38	chr3:111852600-111854000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr3:111852600-111855000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr3:111852600-111856600	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr3:111852600-111857600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:111852800-111853400	Enhancers	Duodenum Mucosa	Duodenum
43	chr3:111852800-111853400	Enhancers	Fetal Muscle Trunk	muscle
44	chr3:111852800-111853400	Enhancers	Pancreas	Pancrea
45	chr3:111852800-111853400	Enhancers	Spleen	Spleen
46	chr3:111852800-111853800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr3:111852800-111856600	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr3:111853000-111853400	Enhancers	Adipose Nuclei	Adipose
49	chr3:111853000-111853400	Enhancers	Left Ventricle	heart
50	chr3:111853000-111853400	Enhancers	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links