Variant report

Variant	rs71427274
Chromosome Location	chr13:30170167-30170168
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:261)
CpG islands
(count:122)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:261 , 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	CTCF	chr13:30170100-30170250	AG09309	skin:	n/a	chr13:30170207-30170220
2	CTCF	chr13:30170060-30170210	AG04450	lung:	n/a	n/a
3	POLR2A	chr13:30168488-30170239	NB4	blood:	n/a	n/a
4	MYC	chr13:30169968-30170184	MCF-7	breast:	n/a	chr13:30169989-30169999
5	CTCF	chr13:30170040-30170190	HA-sp	spinal cord:	n/a	n/a
6	MXI1	chr13:30167583-30170303	IMR90	lung:	n/a	chr13:30167942-30167951
7	POLR2A	chr13:30168329-30170450	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr13:30168504-30170378	GM18526	blood:	n/a	n/a
9	POLR2A	chr13:30168331-30170291	PBDE	blood:	n/a	n/a
10	CTCF	chr13:30170040-30170190	MCF-7	breast:	n/a	n/a
11	CTCF	chr13:30170100-30170250	HPAF	blood vessel:	n/a	chr13:30170207-30170220
12	POLR2A	chr13:30168409-30170279	K562	blood:	n/a	n/a
13	POLR2A	chr13:30168986-30170315	MCF-7	breast:	n/a	n/a
14	TBP	chr13:30168491-30170325	H1-hESC	embryonic stem cell:	n/a	n/a
15	FOXP2	chr13:30169677-30170271	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr13:30168431-30170326	Hela-S3	cervix:	n/a	n/a
17	MAX	chr13:30168336-30170283	MCF-7	breast:	n/a	chr13:30169989-30169999 chr13:30169811-30169820 chr13:30169717-30169726 chr13:30169287-30169296
18	POLR2A	chr13:30168185-30170397	GM12892	blood:	n/a	n/a
19	JUN	chr13:30170096-30170332	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr13:30168413-30170264	HL-60	blood:	n/a	n/a
21	POLR2A	chr13:30169959-30170200	A549	lung:	n/a	n/a
22	MAX	chr13:30169560-30170343	SK-N-SH	brain:	n/a	chr13:30169989-30169999 chr13:30169811-30169820 chr13:30169717-30169726
23	POLR2A	chr13:30168369-30170250	GM12878	blood:	n/a	n/a
24	TAF1	chr13:30168397-30170313	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr13:30170141-30170229	H1-hESC	embryonic stem cell:	n/a	chr13:30170207-30170220
26	ELF1	chr13:30169875-30170228	K562	blood:	n/a	chr13:30169961-30169973 chr13:30169936-30169945
27	CTCF	chr13:30170080-30170230	AG09309	skin:	n/a	chr13:30170207-30170220
28	MAX	chr13:30168302-30170290	NB4	blood:	n/a	chr13:30169989-30169999 chr13:30169811-30169820 chr13:30169717-30169726 chr13:30169287-30169296
29	YY1	chr13:30169607-30170173	H1-hESC	embryonic stem cell:	n/a	chr13:30169937-30169951 chr13:30169936-30169950 chr13:30170042-30170053 chr13:30169936-30169945 chr13:30169964-30169975
30	MAZ	chr13:30168654-30170356	GM12878	blood:	n/a	chr13:30169989-30169999 chr13:30169811-30169820 chr13:30169717-30169726 chr13:30169287-30169296
31	POLR2A	chr13:30168443-30170218	GM12878	blood:	n/a	n/a
32	CTCF	chr13:30170060-30170210	HMF	breast:	n/a	n/a
33	SIN3AK20	chr13:30169893-30170247	SK-N-SH	brain:	n/a	n/a
34	TAF1	chr13:30168871-30170220	HepG2	liver:	n/a	n/a
35	STAT5A	chr13:30169978-30170356	GM12878	blood:	n/a	n/a
36	CTCF	chr13:30170060-30170210	HBMEC	blood vessel:	n/a	n/a
37	POLR2A	chr13:30170052-30170220	H1-hESC	embryonic stem cell:	n/a	n/a
38	PAX5	chr13:30169645-30170242	GM12892	blood:	n/a	n/a
39	POLR2A	chr13:30169017-30170282	H1-neurons	neurons:	n/a	n/a
40	CTCF	chr13:30170100-30170186	Fibrobl	skin:	n/a	n/a
41	NFYB	chr13:30169669-30170297	GM12878	blood:	n/a	n/a
42	USF2	chr13:30170104-30170185	H1-hESC	embryonic stem cell:	n/a	n/a
43	CTCF	chr13:30170060-30170210	GM12878	blood:	n/a	n/a
44	EP300	chr13:30170009-30170278	SK-N-SH_RA	brain:	n/a	n/a
45	CTCF	chr13:30169997-30170256	IMR90	lung:	n/a	chr13:30170207-30170220
46	POLR2A	chr13:30168818-30170192	A549	lung:	n/a	n/a
47	POLR2A	chr13:30169567-30170203	GM12878	blood:	n/a	n/a
48	CTCF	chr13:30170080-30170230	GM12875	blood:	n/a	chr13:30170207-30170220
49	POLR2A	chr13:30168499-30170237	ECC-1	luminal epithelium:	n/a	n/a
50	POLR2A	chr13:30168544-30170271	K562	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:30170129-30170179	ECC-1	luminal epithelium:	n/a
2	chr13:30170122-30170172	HEEpiC	esophagus:	n/a
3	chr13:30170122-30170172	HAEpiC	amniotic membrane:	n/a
4	chr13:30170129-30170179	AG09309	skin:	n/a
5	chr13:30170122-30170172	SKMC	muscle:	n/a
6	chr13:30170122-30170172	IMR90	lung:	fetal
7	chr13:30170122-30170172	SAEC	small airway:	n/a
8	chr13:30170129-30170179	PFSK-1	brain:	n/a
9	chr13:30170122-30170172	PANC-1	pancreas:	n/a
10	chr13:30170122-30170172	HCT-116	colon:	n/a
11	chr13:30170129-30170179	BE2_C	brain:	n/a
12	chr13:30170122-30170172	LNCaP	prostate:	n/a
13	chr13:30170122-30170172	Jurkat	blood:	n/a
14	chr13:30170129-30170179	T-47D	breast:	n/a
15	chr13:30170122-30170172	HNPCEpiC	eye:	n/a
16	chr13:30170129-30170179	HepG2	liver:	n/a
17	chr13:30170122-30170172	HMEC	breast:	n/a
18	chr13:30170122-30170172	U87	brain:	n/a
19	chr13:30170122-30170172	NT2-D1	testis:	n/a
20	chr13:30170129-30170179	HIPEpiC	eye:	n/a
21	chr13:30170122-30170172	T-47D	breast:	n/a
22	chr13:30170122-30170172	BE2_C	brain:	n/a
23	chr13:30170129-30170179	Hepatocyte	liver:	n/a
24	chr13:30170129-30170179	K562	blood:	n/a
25	chr13:30170129-30170179	HNPCEpiC	eye:	n/a
26	chr13:30170122-30170172	HUVEC	blood vessel:	n/a
27	chr13:30170129-30170179	Hela-S3	cervix:	n/a
28	chr13:30170122-30170172	A549	lung:	n/a
29	chr13:30170122-30170172	HepG2	liver:	n/a
30	chr13:30170129-30170179	MCF10A-Er-Src	breast:	n/a
31	chr13:30170129-30170179	LNCaP	prostate:	n/a
32	chr13:30170129-30170179	HCPEpiC	choroid plexus:	n/a
33	chr13:30170122-30170172	BJ	skin:	n/a
34	chr13:30170129-30170179	SKMC	muscle:	n/a
35	chr13:30170129-30170179	HRCEpiC	kidney:	n/a
36	chr13:30170122-30170172	HRPEpiC	eye:	n/a
37	chr13:30170122-30170172	HEK293	kidney:	embryo
38	chr13:30170129-30170179	SK-N-SH_RA	brain:	n/a
39	chr13:30170129-30170179	HCT-116	colon:	n/a
40	chr13:30170129-30170179	U87	brain:	n/a
41	chr13:30170122-30170172	NHDF-neo	bronchial:	n/a
42	chr13:30170129-30170179	ProgFib	skin:	n/a
43	chr13:30170129-30170179	GM12892	blood:	n/a
44	chr13:30170129-30170179	NHBE	bronchial:	n/a
45	chr13:30170129-30170179	MCF-7	breast:	n/a
46	chr13:30170129-30170179	RPTEC	kidney:	n/a
47	chr13:30170122-30170172	NHBE	bronchial:	n/a
48	chr13:30170122-30170172	HIPEpiC	eye:	n/a
49	chr13:30170129-30170179	HRPEpiC	eye:	n/a
50	chr13:30170129-30170179	NT2-D1	testis:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:30093611..30096522-chr13:30167989..30170777,2	MCF-7	breast:
2	chr13:30169255..30170193-chr3:73159968..73160573,2	Hela-S3	cervix:
3	chr13:30168902..30170623-chr13:47369921..47372567,2	MCF-7	breast:
4	chr13:30069723..30071518-chr13:30169502..30172461,2	MCF-7	breast:
5	chr13:30169260..30170181-chr14:23398301..23399025,2	HCT-116	colon:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MTUS2-2	chr13:30170020-30170280	XLOC_010330

No data

Variant related genes	Relation type
SLC7A1	TF binding region
SLC7A1	CpG island
ENSG00000139514	Chromatin interaction
ENSG00000223247	Chromatin interaction
ENSG00000100462	Chromatin interaction
ENSG00000132938	Chromatin interaction
ENSG00000257285	Chromatin interaction
ENSG00000139684	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10220050	1.00[ASN][1000 genomes]
rs10220112	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10492457	1.00[ASN][1000 genomes]
rs12853894	1.00[ASN][1000 genomes]
rs12864282	1.00[ASN][1000 genomes]
rs12865724	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12866411	1.00[ASN][1000 genomes]
rs12868072	1.00[ASN][1000 genomes]
rs12872620	1.00[ASN][1000 genomes]
rs12872872	1.00[ASN][1000 genomes]
rs12873674	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12877965	1.00[ASN][1000 genomes]
rs13378570	1.00[ASN][1000 genomes]
rs2036973	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2669038	1.00[ASN][1000 genomes]
rs3011607	1.00[ASN][1000 genomes]
rs34117941	1.00[ASN][1000 genomes]
rs34148142	1.00[ASN][1000 genomes]
rs34220342	1.00[ASN][1000 genomes]
rs34492142	1.00[ASN][1000 genomes]
rs34967062	1.00[ASN][1000 genomes]
rs34973257	1.00[ASN][1000 genomes]
rs34978805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35033033	1.00[ASN][1000 genomes]
rs35227498	1.00[ASN][1000 genomes]
rs35566813	1.00[ASN][1000 genomes]
rs35569918	1.00[ASN][1000 genomes]
rs35809262	1.00[ASN][1000 genomes]
rs35820783	1.00[ASN][1000 genomes]
rs35901321	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs478085	1.00[ASN][1000 genomes]
rs555913	1.00[ASN][1000 genomes]
rs71427278	1.00[ASN][1000 genomes]
rs71427279	1.00[ASN][1000 genomes]
rs71427280	1.00[ASN][1000 genomes]
rs71434735	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71434744	1.00[ASN][1000 genomes]
rs71434746	1.00[ASN][1000 genomes]
rs7320198	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73454227	1.00[ASN][1000 genomes]
rs74042085	1.00[ASN][1000 genomes]
rs7986326	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7991247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7991463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7992028	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7992839	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998704	1.00[ASN][1000 genomes]
rs9314960	1.00[ASN][1000 genomes]
rs9314961	1.00[ASN][1000 genomes]
rs9314962	1.00[ASN][1000 genomes]
rs9314964	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9314968	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9578108	1.00[ASN][1000 genomes]
rs9578110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9578112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9578118	1.00[ASN][1000 genomes]
rs9578121	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9578122	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9578123	1.00[ASN][1000 genomes]
rs9578125	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9578127	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9578128	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9578130	1.00[ASN][1000 genomes]
rs9578131	1.00[ASN][1000 genomes]
rs9578133	1.00[ASN][1000 genomes]
rs9578134	1.00[ASN][1000 genomes]
rs9579405	1.00[ASN][1000 genomes]
rs9579406	1.00[ASN][1000 genomes]
rs9579407	1.00[ASN][1000 genomes]
rs9579408	1.00[ASN][1000 genomes]
rs9579410	1.00[ASN][1000 genomes]
rs9579411	1.00[ASN][1000 genomes]
rs9579413	1.00[ASN][1000 genomes]
rs9579414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9579417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9579418	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9579419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9579424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9579425	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9579428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9579439	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9579440	1.00[ASN][1000 genomes]
rs9579442	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9579445	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9579446	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9579447	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9579449	0.85[AFR][1000 genomes]
rs9579451	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9579454	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9579455	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9579457	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9579459	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9579462	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9579463	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9579464	1.00[ASN][1000 genomes]
rs9579465	1.00[ASN][1000 genomes]
rs9579466	1.00[ASN][1000 genomes]
rs9579468	1.00[ASN][1000 genomes]
rs9579470	1.00[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	esv3420380	chr13:30168177-30170725	Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv3359253	chr13:30168577-30171125	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv3445424	chr13:30169002-30170950	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30167400-30170400	Active TSS	H1 Cell Line	embryonic stem cell
2	chr13:30167400-30170400	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr13:30167600-30170200	Active TSS	GM12878-XiMat	blood
4	chr13:30167600-30170400	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr13:30167600-30170400	Active TSS	A549	lung
6	chr13:30167600-30170400	Active TSS	Hela-S3	cervix
7	chr13:30167600-30170600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr13:30167800-30170400	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr13:30167800-30170600	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr13:30168000-30170200	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr13:30168000-30170400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr13:30168000-30170400	Active TSS	K562	blood
13	chr13:30168200-30170200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr13:30168200-30170200	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr13:30168200-30170400	Active TSS	H9 Cell Line	embryonic stem cell
16	chr13:30168200-30170400	Active TSS	Right Ventricle	heart
17	chr13:30168200-30170600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr13:30168200-30170600	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr13:30168200-30170600	Active TSS	Fetal Brain Female	brain
20	chr13:30168400-30170200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr13:30168400-30170200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr13:30168400-30170200	Active TSS	Brain Angular Gyrus	brain
23	chr13:30168400-30170200	Active TSS	Brain Cingulate Gyrus	brain
24	chr13:30168400-30170200	Active TSS	Fetal Kidney	kidney
25	chr13:30168400-30170200	Active TSS	Fetal Stomach	stomach
26	chr13:30168400-30170200	Active TSS	Gastric	stomach
27	chr13:30168400-30170200	Active TSS	Left Ventricle	heart
28	chr13:30168400-30170400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr13:30168400-30170400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr13:30168400-30170400	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr13:30168400-30170400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr13:30168400-30170400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr13:30168400-30170400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr13:30168400-30170400	Active TSS	Aorta	Aorta
35	chr13:30168400-30170400	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr13:30168400-30170400	Active TSS	Esophagus	oesophagus
37	chr13:30168400-30170400	Active TSS	Fetal Intestine Large	intestine
38	chr13:30168400-30170400	Active TSS	Pancreas	Pancrea
39	chr13:30168400-30170400	Active TSS	NHLF	lung
40	chr13:30168400-30170600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr13:30168400-30170600	Active TSS	Brain Anterior Caudate	brain
42	chr13:30168400-30170800	Active TSS	Colonic Mucosa	Colon
43	chr13:30168600-30170200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr13:30168600-30170200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr13:30168600-30170200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr13:30168600-30170200	Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr13:30168600-30170200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr13:30168600-30170200	Active TSS	NHEK	skin
49	chr13:30168600-30170400	Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr13:30168600-30170400	Active TSS	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links