Variant report

Variant	rs7497201
Chromosome Location	chr15:75190690-75190691
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:62)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:62 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:75187779-75190960	K562	blood:	n/a	n/a
2	POLR2A	chr15:75189238-75190889	HepG2	liver:	n/a	n/a
3	POLR2A	chr15:75187739-75194836	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr15:75189183-75190865	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr15:75190611-75190859	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr15:75187943-75190750	HUVEC	blood vessel:	n/a	n/a
7	CTCF	chr15:75190600-75190750	HBMEC	blood vessel:	n/a	n/a
8	PML	chr15:75189958-75190850	GM12878	blood:	n/a	n/a
9	POLR2A	chr15:75189679-75190904	HCT-116	colon:	n/a	n/a
10	POLR2A	chr15:75188853-75190851	K562	blood:	n/a	n/a
11	POLR2A	chr15:75188189-75190877	GM12878	blood:	n/a	n/a
12	POLR2A	chr15:75189258-75190898	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr15:75188363-75190846	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr15:75190674-75190804	HepG2	liver:	n/a	n/a
15	POLR2A	chr15:75188605-75190890	U87	brain:	n/a	n/a
16	POLR2A	chr15:75189198-75190897	HL-60	blood:	n/a	n/a
17	POLR2A	chr15:75188901-75190853	HCT-116	colon:	n/a	n/a
18	POLR2A	chr15:75188926-75194641	U87	brain:	n/a	n/a
19	POLR2A	chr15:75187964-75190840	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr15:75188787-75190852	K562	blood:	n/a	n/a
21	POLR2A	chr15:75190672-75190831	A549	lung:	n/a	n/a
22	POLR2A	chr15:75188309-75190832	GM12891	blood:	n/a	n/a
23	POLR2A	chr15:75188017-75190928	K562	blood:	n/a	n/a
24	POLR2A	chr15:75189424-75190741	HEK293	kidney:	n/a	n/a
25	POLR2A	chr15:75189228-75190774	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr15:75188187-75190911	K562	blood:	n/a	n/a
27	POLR2A	chr15:75188926-75193508	U87	brain:	n/a	n/a
28	POLR2A	chr15:75187473-75194577	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr15:75188765-75190977	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr15:75187941-75190956	HepG2	liver:	n/a	n/a
31	POLR2A	chr15:75188632-75190816	K562	blood:	n/a	n/a
32	POLR2A	chr15:75187279-75194196	HepG2	liver:	n/a	n/a
33	POLR2A	chr15:75188313-75190881	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr15:75188157-75190930	GM12878	blood:	n/a	n/a
35	POLR2A	chr15:75188079-75191035	GM12892	blood:	n/a	n/a
36	POLR2A	chr15:75190456-75190815	GM12878	blood:	n/a	n/a
37	POLR2A	chr15:75188563-75190883	K562	blood:	n/a	n/a
38	POLR2A	chr15:75187680-75194520	SK-N-MC	brain:	n/a	n/a
39	POLR2A	chr15:75188612-75190883	MCF-7	breast:	n/a	n/a
40	POLR2A	chr15:75188556-75193697	PANC-1	pancreas:	n/a	n/a
41	POLR2A	chr15:75189540-75190876	HUVEC	blood vessel:	n/a	n/a
42	POLR2A	chr15:75188170-75190915	SK-N-SH	brain:	n/a	n/a
43	POLR2A	chr15:75190673-75190846	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr15:75189225-75190852	A549	lung:	n/a	n/a
45	POLR2A	chr15:75189510-75190934	HL-60	blood:	n/a	n/a
46	POLR2A	chr15:75188606-75191085	GM12892	blood:	n/a	n/a
47	POLR2A	chr15:75190602-75190872	A549	lung:	n/a	n/a
48	POLR2A	chr15:75190638-75190888	HepG2	liver:	n/a	n/a
49	POLR2A	chr15:75188118-75190973	PANC-1	pancreas:	n/a	n/a
50	POLR2A	chr15:75189778-75190730	SK-N-MC	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:75131329..75142649-chr15:75180088..75200119,60	MCF-7	breast:
2	chr15:75181107..75185393-chr15:75190667..75200295,16	MCF-7	breast:
3	chr15:75165443..75167365-chr15:75189405..75191280,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000260824	TF binding region
ENSG00000140474	Chromatin interaction
ENSG00000140497	Chromatin interaction
ENSG00000178802	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12442901	0.88[GIH][hapmap]
rs12906946	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12911781	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12914369	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1378938	0.88[GIH][hapmap]
rs1869959	0.87[CEU][hapmap];0.81[YRI][hapmap]
rs2168519	0.85[GIH][hapmap]
rs2301249	0.85[GIH][hapmap]
rs4886615	0.83[CEU][hapmap];0.88[GIH][hapmap]
rs4886619	0.83[GIH][hapmap]
rs4886633	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6495124	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6495126	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6495127	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495131	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67411922	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7085	0.88[GIH][hapmap]
rs7162232	0.85[GIH][hapmap]
rs7174968	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7176022	0.83[GIH][hapmap]
rs7180484	0.88[GIH][hapmap]
rs7495033	0.93[EUR][1000 genomes]
rs8025890	0.81[AFR][1000 genomes]
rs8031937	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8033381	0.85[GIH][hapmap]
rs8042694	0.92[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9210	0.83[CEU][hapmap];0.86[GIH][hapmap]
rs936228	0.83[CEU][hapmap];0.88[GIH][hapmap]
rs936229	0.83[CEU][hapmap];0.88[GIH][hapmap]
rs936230	0.87[CEU][hapmap];0.95[GIH][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904381	chr15:75108636-75242155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7497201	MPI	cis	lymphoblastoid	seeQTL
rs7497201	ULK3	cis	Whole Blood	GTEx
rs7497201	C15orf17	cis	lymphoblastoid	seeQTL
rs7497201	MPI	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75183200-75191600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr15:75183200-75192000	Weak transcription	Fetal Kidney	kidney
3	chr15:75183200-75192400	Weak transcription	HUVEC	blood vessel
4	chr15:75183200-75197600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:75183400-75192200	Weak transcription	NH-A	brain
6	chr15:75183600-75193800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr15:75183600-75193800	Strong transcription	Fetal Stomach	stomach
8	chr15:75184000-75195400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:75184200-75192400	Weak transcription	Fetal Brain Male	brain
10	chr15:75184200-75196600	Weak transcription	Small Intestine	intestine
11	chr15:75185000-75193800	Strong transcription	Fetal Intestine Small	intestine
12	chr15:75185000-75194800	Weak transcription	Right Atrium	heart
13	chr15:75185200-75193800	Strong transcription	Fetal Intestine Large	intestine
14	chr15:75185200-75197000	Weak transcription	Fetal Heart	heart
15	chr15:75185800-75191200	Weak transcription	Aorta	Aorta
16	chr15:75185800-75192600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:75186200-75191200	Weak transcription	Placenta	Placenta
18	chr15:75186200-75191200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr15:75186200-75191600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr15:75186200-75192000	Weak transcription	NHDF-Ad	bronchial
21	chr15:75186200-75192400	Weak transcription	Colon Smooth Muscle	Colon
22	chr15:75186200-75193600	Weak transcription	Stomach Mucosa	stomach
23	chr15:75186400-75191600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr15:75186400-75191800	Weak transcription	Primary B cells from cord blood	blood
25	chr15:75186800-75195800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr15:75187000-75192400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr15:75187200-75193400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr15:75187200-75193600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr15:75187400-75193600	Strong transcription	Stomach Smooth Muscle	stomach
30	chr15:75187600-75193600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:75187600-75193800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr15:75187600-75197200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr15:75187800-75193600	Strong transcription	Primary T cells from cord blood	blood
34	chr15:75187800-75193800	Strong transcription	Duodenum Mucosa	Duodenum
35	chr15:75187800-75193800	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr15:75187800-75194000	Strong transcription	A549	lung
37	chr15:75187800-75196600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr15:75187800-75196800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr15:75187800-75197400	Strong transcription	Fetal Thymus	thymus
40	chr15:75188000-75191200	Strong transcription	GM12878-XiMat	blood
41	chr15:75188000-75192800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr15:75188000-75193400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr15:75188000-75193600	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr15:75188000-75193600	Strong transcription	Liver	Liver
45	chr15:75188000-75193800	Strong transcription	Brain Hippocampus Middle	brain
46	chr15:75188000-75193800	Strong transcription	K562	blood
47	chr15:75188000-75196000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr15:75188000-75196800	Strong transcription	Brain Germinal Matrix	brain
49	chr15:75188000-75197000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr15:75188000-75197000	Strong transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links