Variant report

Variant	rs2003344
Chromosome Location	chr15:76632301-76632302
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:122)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:76631682-76632446	HL-60	blood:	n/a	n/a
2	POLR2A	chr15:76628957-76633759	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr15:76631377-76633541	H1-neurons	neurons:	n/a	n/a
4	SUZ12	chr15:76628987-76637136	NT2-D1	testis:	n/a	n/a
5	POLR2A	chr15:76632133-76632532	K562	blood:	n/a	n/a
6	CTBP2	chr15:76631455-76635500	H1-hESC	embryonic stem cell:	n/a	n/a
7	SUZ12	chr15:76629195-76634787	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr15:76631898-76633726	GM18951	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:76632287-76632337	HCT-116	colon:	n/a
2	chr15:76632292-76632342	Hepatocyte	liver:	n/a
3	chr15:76632287-76632337	HepG2	liver:	n/a
4	chr15:76632292-76632342	HCF	heart:	n/a
5	chr15:76632292-76632342	SK-N-MC	brain:	n/a
6	chr15:76632287-76632337	GM12892	blood:	n/a
7	chr15:76632292-76632342	HRE	kidney:	n/a
8	chr15:76632287-76632337	AG04450	lung:	fetal
9	chr15:76632287-76632337	HIPEpiC	eye:	n/a
10	chr15:76632287-76632337	HRPEpiC	eye:	n/a
11	chr15:76632292-76632342	PFSK-1	brain:	n/a
12	chr15:76632287-76632337	HPAEpiC	pulmonary alveolar:	n/a
13	chr15:76632292-76632342	A549	lung:	n/a
14	chr15:76632287-76632337	H1-hESC	embryonic stem cell:	embryo
15	chr15:76632292-76632342	U87	brain:	n/a
16	chr15:76632292-76632342	HCM	heart:	n/a
17	chr15:76632287-76632337	HUVEC	blood vessel:	n/a
18	chr15:76632287-76632337	SK-N-SH_RA	brain:	n/a
19	chr15:76632292-76632342	GM06990	blood:	n/a
20	chr15:76632292-76632342	NHDF-neo	bronchial:	n/a
21	chr15:76632287-76632337	HCM	heart:	n/a
22	chr15:76632287-76632337	GM12891	blood:	n/a
23	chr15:76632287-76632337	AoSMC	blood vessel:	n/a
24	chr15:76632292-76632342	HUVEC	blood vessel:	n/a
25	chr15:76632292-76632342	HAEpiC	amniotic membrane:	n/a
26	chr15:76632287-76632337	T-47D	breast:	n/a
27	chr15:76632287-76632337	NB4	blood:	n/a
28	chr15:76632292-76632342	T-47D	breast:	n/a
29	chr15:76632292-76632342	PrEC	prostate:	n/a
30	chr15:76632292-76632342	AoSMC	blood vessel:	n/a
31	chr15:76632287-76632337	SK-N-SH	brain:	n/a
32	chr15:76632292-76632342	HMEC	breast:	n/a
33	chr15:76632287-76632337	NT2-D1	testis:	n/a
34	chr15:76632292-76632342	MCF10A-Er-Src	breast:	n/a
35	chr15:76632292-76632342	BJ	skin:	n/a
36	chr15:76632287-76632337	MCF10A-Er-Src	breast:	n/a
37	chr15:76632292-76632342	Caco-2	colon:	n/a
38	chr15:76632292-76632342	HCT-116	colon:	n/a
39	chr15:76632287-76632337	U87	brain:	n/a
40	chr15:76632287-76632337	RPTEC	kidney:	n/a
41	chr15:76632287-76632337	HCF	heart:	n/a
42	chr15:76632287-76632337	Hela-S3	cervix:	n/a
43	chr15:76632287-76632337	HEEpiC	esophagus:	n/a
44	chr15:76632287-76632337	HNPCEpiC	eye:	n/a
45	chr15:76632292-76632342	AG09309	skin:	n/a
46	chr15:76632292-76632342	ovcar-3	ovarian:	n/a
47	chr15:76632292-76632342	AG09319	gingival:	n/a
48	chr15:76632292-76632342	ProgFib	skin:	n/a
49	chr15:76632292-76632342	HepG2	liver:	n/a
50	chr15:76632292-76632342	NHBE	bronchial:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:76601310..76610583-chr15:76618699..76634643,40	K562	blood:
2	chr15:76628671..76632944-chr15:76633969..76642252,10	MCF-7	breast:
3	chr15:76601574..76614388-chr15:76623703..76634730,38	K562	blood:
4	chr15:76627980..76632315-chr15:76633215..76636196,5	MCF-7	breast:
5	chr15:76630323..76632934-chr15:77355490..77357171,2	K562	blood:
6	chr15:76630618..76633246-chr15:76671829..76673785,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000270036	TF binding region
ENSG00000270036	CpG island
ENSG00000259514	Chromatin interaction
ENSG00000270036	Chromatin interaction
ENSG00000140374	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11072591	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11072597	0.81[AMR][1000 genomes]
rs11072598	0.81[AMR][1000 genomes]
rs11629888	0.84[AMR][1000 genomes]
rs11632222	0.84[AMR][1000 genomes]
rs11634019	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11635463	0.81[AMR][1000 genomes]
rs11637490	0.82[AMR][1000 genomes]
rs11638767	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11855999	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857015	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11857327	0.81[AMR][1000 genomes]
rs12900179	0.85[AMR][1000 genomes]
rs12903874	0.85[AMR][1000 genomes]
rs12906143	0.84[AMR][1000 genomes]
rs1607015	0.84[AMR][1000 genomes]
rs2280306	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2957614	0.80[AMR][1000 genomes]
rs3765115	0.87[AMR][1000 genomes]
rs4886493	0.87[AMR][1000 genomes]
rs4886495	0.84[AMR][1000 genomes]
rs4886798	0.86[AMR][1000 genomes]
rs4886805	0.83[AMR][1000 genomes]
rs56246286	0.85[AMR][1000 genomes]
rs62028380	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62028406	0.85[AMR][1000 genomes]
rs62028423	0.82[AMR][1000 genomes]
rs71405204	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs908817	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904399	chr15:76622903-76646575	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv827391	chr15:76626571-76636327	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2003344	SCAPER	cis	Esophagus Muscularis	GTEx
rs2003344	SCAPER	cis	Artery Tibial	GTEx
rs2003344	SCAPER	cis	Adipose Subcutaneous	GTEx
rs2003344	SCAPER	cis	Whole Blood	GTEx
rs2003344	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs2003344	SCAPER	cis	Thyroid	GTEx
rs2003344	SCAPER	cis	Nerve Tibial	GTEx
rs2003344	SCAPER	cis	lung	GTEx
rs2003344	SCAPER	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76627400-76635400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr15:76627600-76632400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
3	chr15:76627600-76634400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
4	chr15:76629000-76633600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
5	chr15:76629200-76632600	Bivalent Enhancer	Fetal Thymus	thymus
6	chr15:76629400-76633400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
7	chr15:76629800-76632800	Bivalent Enhancer	Stomach Mucosa	stomach
8	chr15:76630200-76641800	Weak transcription	A549	lung
9	chr15:76630400-76632600	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
10	chr15:76630400-76636400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:76630600-76632400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
12	chr15:76630600-76635600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:76630800-76632400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr15:76631000-76632600	Bivalent Enhancer	Liver	Liver
15	chr15:76631200-76632600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
16	chr15:76631200-76633400	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
17	chr15:76631400-76632600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr15:76631400-76633600	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
19	chr15:76631600-76632600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
20	chr15:76631600-76632600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
21	chr15:76631600-76633200	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
22	chr15:76631600-76633600	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
23	chr15:76631600-76634800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
24	chr15:76631600-76636400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:76631800-76632400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
26	chr15:76631800-76632800	Weak transcription	Hela-S3	cervix
27	chr15:76631800-76633600	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
28	chr15:76631800-76633600	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
29	chr15:76631800-76633600	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
30	chr15:76631800-76634400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
31	chr15:76631800-76634400	Strong transcription	K562	blood
32	chr15:76631800-76635600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
33	chr15:76632000-76632400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
34	chr15:76632000-76632400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr15:76632000-76632400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
36	chr15:76632000-76632400	Bivalent Enhancer	Brain Germinal Matrix	brain
37	chr15:76632000-76632400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
38	chr15:76632000-76632400	Bivalent/Poised TSS	Thymus	Thymus
39	chr15:76632000-76632400	Flanking Active TSS	GM12878-XiMat	blood
40	chr15:76632000-76632600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr15:76632000-76632600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
42	chr15:76632000-76632800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr15:76632000-76632800	Bivalent/Poised TSS	Fetal Stomach	stomach
44	chr15:76632000-76632800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
45	chr15:76632000-76633200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
46	chr15:76632000-76633200	Active TSS	HSMM	muscle
47	chr15:76632000-76633400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
48	chr15:76632000-76633600	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
49	chr15:76632000-76633600	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
50	chr15:76632000-76633600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin

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