Variant report

Variant	rs13078131
Chromosome Location	chr3:47204939-47204940
allele	G/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	MYBL2	chr3:47204479-47205009	HepG2	liver:	n/a	n/a
2	BCLAF1	chr3:47204267-47205023	GM12878	blood:	n/a	chr3:47204624-47204633 chr3:47204976-47204989 chr3:47204781-47204794
3	YY1	chr3:47204498-47206409	GM12878	blood:	n/a	chr3:47205587-47205598 chr3:47205468-47205479 chr3:47205189-47205198 chr3:47205321-47205332 chr3:47205279-47205293 chr3:47205256-47205270 chr3:47204848-47204862 chr3:47205252-47205266 chr3:47205258-47205267 chr3:47205253-47205267 chr3:47205109-47205118
4	MAZ	chr3:47204647-47206459	Hela-S3	cervix:	n/a	chr3:47205889-47205899
5	PAX5	chr3:47204710-47206375	GM12892	blood:	n/a	n/a
6	MAX	chr3:47204474-47206415	K562	blood:	n/a	chr3:47205889-47205899
7	SIN3AK20	chr3:47204525-47206286	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr3:47204597-47206503	H1-neurons	neurons:	n/a	n/a
9	TEAD4	chr3:47204732-47206081	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr3:47204777-47206501	K562	blood:	n/a	n/a
11	MYC	chr3:47204469-47206552	K562	blood:	n/a	chr3:47205889-47205899
12	YY1	chr3:47204499-47205030	GM12892	blood:	n/a	chr3:47204848-47204862
13	ELK4	chr3:47204522-47205027	Hela-S3	cervix:	n/a	chr3:47204725-47204736
14	MYC	chr3:47204783-47206024	MCF-7	breast:	n/a	chr3:47205889-47205899
15	MAX	chr3:47204399-47206611	HCT-116	colon:	n/a	chr3:47205889-47205899
16	REST	chr3:47204200-47206694	H1-neurons	neurons:	n/a	chr3:47205082-47205095
17	POLR2A	chr3:47204689-47206436	Hela-S3	cervix:	n/a	n/a
18	MAX	chr3:47204759-47205488	K562	blood:	n/a	n/a
19	REST	chr3:47204760-47204975	SK-N-SH	brain:	n/a	n/a
20	YY1	chr3:47204531-47206395	K562	blood:	n/a	chr3:47205587-47205598 chr3:47205468-47205479 chr3:47205189-47205198 chr3:47205321-47205332 chr3:47205279-47205293 chr3:47205256-47205270 chr3:47204848-47204862 chr3:47205252-47205266 chr3:47205258-47205267 chr3:47205253-47205267 chr3:47205109-47205118
21	MYC	chr3:47204271-47205286	A549	lung:	n/a	n/a
22	CHD1	chr3:47204412-47206570	H1-hESC	embryonic stem cell:	n/a	chr3:47205244-47205254
23	SP1	chr3:47204733-47205087	A549	lung:	n/a	n/a
24	POLR2A	chr3:47204540-47204982	GM12892	blood:	n/a	n/a
25	POLR2A	chr3:47204896-47206417	PBDE	blood:	n/a	n/a
26	YY1	chr3:47204554-47206440	GM12892	blood:	n/a	chr3:47205587-47205598 chr3:47205468-47205479 chr3:47205189-47205198 chr3:47205321-47205332 chr3:47205279-47205293 chr3:47205256-47205270 chr3:47204848-47204862 chr3:47205252-47205266 chr3:47205258-47205267 chr3:47205253-47205267 chr3:47205109-47205118
27	HDAC2	chr3:47204615-47204951	HepG2	liver:	n/a	n/a
28	ELF1	chr3:47204591-47204947	MCF-7	breast:	n/a	chr3:47204892-47204904 chr3:47204724-47204735 chr3:47204724-47204735
29	POLR2A	chr3:47204607-47206336	GM18505	blood:	n/a	n/a
30	MAZ	chr3:47204296-47206660	K562	blood:	n/a	chr3:47205889-47205899
31	TAF1	chr3:47204551-47205143	SK-N-SH	brain:	n/a	n/a
32	TAF1	chr3:47204710-47206155	H1-hESC	embryonic stem cell:	n/a	n/a
33	GABPA	chr3:47204559-47205354	K562	blood:	n/a	chr3:47204634-47204641
34	TAF1	chr3:47204597-47206392	K562	blood:	n/a	n/a
35	E2F4	chr3:47204760-47206373	K562	blood:	n/a	chr3:47206096-47206106 chr3:47205893-47205903 chr3:47205189-47205198 chr3:47205258-47205267
36	TBP	chr3:47204299-47206472	K562	blood:	n/a	n/a
37	TBL1XR1	chr3:47204325-47206538	GM12878	blood:	n/a	n/a
38	MTA3	chr3:47204504-47205047	GM12878	blood:	n/a	n/a
39	SIN3A	chr3:47204091-47206719	H1-hESC	embryonic stem cell:	n/a	chr3:47205749-47205760 chr3:47206305-47206316 chr3:47205587-47205598
40	POLR2A	chr3:47204906-47206102	ProgFib	skin:	n/a	n/a
41	NFATC1	chr3:47204618-47205089	GM12878	blood:	n/a	n/a
42	HCFC1	chr3:47204218-47206975	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr3:47204595-47206417	HL-60	blood:	n/a	n/a
44	POLR2A	chr3:47204713-47206483	K562	blood:	n/a	n/a
45	CREB1	chr3:47204784-47206404	K562	blood:	n/a	n/a
46	STAT5A	chr3:47204695-47205040	GM12878	blood:	n/a	n/a
47	CCNT2	chr3:47204688-47206434	K562	blood:	n/a	chr3:47205817-47205826 chr3:47205083-47205092 chr3:47205468-47205477 chr3:47205473-47205482
48	HCFC1	chr3:47204645-47206766	K562	blood:	n/a	n/a
49	CHD1	chr3:47203409-47206971	IMR90	lung:	n/a	chr3:47205244-47205254
50	POLR2A	chr3:47204769-47206095	A549	lung:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:47204927-47204977	GM12878	blood:	n/a
2	chr3:47204927-47204977	HEK293	kidney:	embryo
3	chr3:47204927-47204977	HUVEC	blood vessel:	n/a
4	chr3:47204927-47204977	SK-N-SH_RA	brain:	n/a
5	chr3:47204927-47204977	GM12891	blood:	n/a
6	chr3:47204927-47204977	PANC-1	pancreas:	n/a
7	chr3:47204927-47204977	H1-hESC	embryonic stem cell:	embryo
8	chr3:47204927-47204977	HRPEpiC	eye:	n/a
9	chr3:47204927-47204977	T-47D	breast:	n/a
10	chr3:47204927-47204977	IMR90	lung:	fetal
11	chr3:47204927-47204977	NHDF-neo	bronchial:	n/a
12	chr3:47204927-47204977	K562	blood:	n/a
13	chr3:47204927-47204977	HRE	kidney:	n/a
14	chr3:47204927-47204977	MCF-7	breast:	n/a
15	chr3:47204927-47204977	Caco-2	colon:	n/a
16	chr3:47204927-47204977	Hela-S3	cervix:	n/a
17	chr3:47204927-47204977	Hepatocyte	liver:	n/a
18	chr3:47204927-47204977	HCF	heart:	n/a
19	chr3:47204927-47204977	HIPEpiC	eye:	n/a
20	chr3:47204927-47204977	SAEC	small airway:	n/a
21	chr3:47204927-47204977	Jurkat	blood:	n/a
22	chr3:47204927-47204977	HRCEpiC	kidney:	n/a
23	chr3:47204927-47204977	U87	brain:	n/a
24	chr3:47204927-47204977	AG04449	skin:	fetal
25	chr3:47204927-47204977	HEEpiC	esophagus:	n/a
26	chr3:47204927-47204977	GM12892	blood:	n/a
27	chr3:47204927-47204977	CMK	blood:	n/a
28	chr3:47204927-47204977	HMEC	breast:	n/a
29	chr3:47204927-47204977	ovcar-3	ovarian:	n/a
30	chr3:47204927-47204977	AG09319	gingival:	n/a
31	chr3:47204927-47204977	ProgFib	skin:	n/a
32	chr3:47204927-47204977	GM19239	blood:	n/a
33	chr3:47204927-47204977	NT2-D1	testis:	n/a
34	chr3:47204927-47204977	AoSMC	blood vessel:	n/a
35	chr3:47204927-47204977	PFSK-1	brain:	n/a
36	chr3:47204927-47204977	RPTEC	kidney:	n/a
37	chr3:47204927-47204977	HPAEpiC	pulmonary alveolar:	n/a
38	chr3:47204927-47204977	HCM	heart:	n/a
39	chr3:47204927-47204977	HNPCEpiC	eye:	n/a
40	chr3:47204927-47204977	HCT-116	colon:	n/a
41	chr3:47204927-47204977	BE2_C	brain:	n/a
42	chr3:47204927-47204977	SKMC	muscle:	n/a
43	chr3:47204927-47204977	HL-60	blood:	n/a
44	chr3:47204927-47204977	ECC-1	luminal epithelium:	n/a
45	chr3:47204927-47204977	NB4	blood:	n/a
46	chr3:47204927-47204977	AG09309	skin:	n/a
47	chr3:47204927-47204977	HAEpiC	amniotic membrane:	n/a
48	chr3:47204927-47204977	A549	lung:	n/a
49	chr3:47204927-47204977	SK-N-SH	brain:	n/a
50	chr3:47204927-47204977	NHBE	bronchial:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:47047075..47049174-chr3:47204688..47207568,2	K562	blood:
2	chr3:47203222..47204974-chr3:47216567..47218199,2	K562	blood:
3	chr3:47204122..47207133-chr3:47321636..47325818,4	K562	blood:
4	chr3:47204211..47206785-chr3:47421682..47423744,2	K562	blood:
5	chr3:47203577..47205455-chr3:47421565..47423969,3	MCF-7	breast:
6	chr3:47204839..47206673-chr3:47316671..47318992,2	K562	blood:

Variant related genes	Relation type
KIF9-AS1	TF binding region
KIF9-AS1	CpG island
ENSG00000088727	Chromatin interaction
ENSG00000076201	Chromatin interaction
ENSG00000114648	Chromatin interaction
ENSG00000260236	Chromatin interaction
ENSG00000160796	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11130114	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11130115	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11708451	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11712716	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11714282	0.83[ASN][1000 genomes]
rs11714373	0.81[EUR][1000 genomes]
rs11716539	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11718795	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11719306	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11719738	0.82[EUR][1000 genomes]
rs12488225	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12489211	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12493425	0.82[EUR][1000 genomes]
rs12629262	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12635619	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13061071	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13062022	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13063250	0.80[ASN][1000 genomes]
rs13084117	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13094438	0.81[ASN][1000 genomes]
rs13094672	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13098228	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1811652	0.82[EUR][1000 genomes]
rs2132173	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2276853	0.81[ASN][1000 genomes]
rs2276854	0.81[ASN][1000 genomes]
rs4078466	0.80[EUR][1000 genomes]
rs4082155	0.81[EUR][1000 genomes]
rs4682852	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4683320	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4683324	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58956475	0.81[EUR][1000 genomes]
rs62246451	0.82[EUR][1000 genomes]
rs6442059	0.82[EUR][1000 genomes]
rs6766230	0.82[EUR][1000 genomes]
rs6767907	0.81[EUR][1000 genomes]
rs6772670	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6785790	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6791062	0.80[EUR][1000 genomes]
rs6791842	0.80[ASN][1000 genomes]
rs7615323	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7621911	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9818382	0.82[EUR][1000 genomes]
rs9821119	0.82[EUR][1000 genomes]
rs9837343	0.82[EUR][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	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv590210	chr3:47126543-47214122	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv590211	chr3:47189485-47256057	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv3801	chr3:47201530-47246438	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13078131	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs13078131	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47203000-47207600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:47203200-47205800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:47203200-47207400	Active TSS	GM12878-XiMat	blood
4	chr3:47203200-47207600	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr3:47203400-47207200	Active TSS	Ovary	ovary
6	chr3:47203600-47205000	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr3:47203600-47205200	Active TSS	Right Atrium	heart
8	chr3:47203600-47206600	Active TSS	Right Ventricle	heart
9	chr3:47203600-47207200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:47203600-47207200	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr3:47203600-47207200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:47203600-47207200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:47203600-47207200	Active TSS	HSMMtube	muscle
14	chr3:47203800-47206000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:47203800-47206600	Active TSS	Brain Germinal Matrix	brain
16	chr3:47203800-47206600	Active TSS	Fetal Thymus	thymus
17	chr3:47203800-47207000	Active TSS	Psoas Muscle	Psoas
18	chr3:47203800-47207200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:47203800-47207200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:47203800-47207200	Active TSS	Fetal Intestine Large	intestine
21	chr3:47203800-47207200	Active TSS	Fetal Intestine Small	intestine
22	chr3:47203800-47207200	Active TSS	Stomach Smooth Muscle	stomach
23	chr3:47203800-47207600	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr3:47203800-47207600	Active TSS	H1 Cell Line	embryonic stem cell
25	chr3:47203800-47207600	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr3:47204000-47205400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:47204000-47206600	Active TSS	Sigmoid Colon	Sigmoid Colon
28	chr3:47204000-47206800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:47204000-47206800	Active TSS	Fetal Muscle Leg	muscle
30	chr3:47204000-47206800	Active TSS	Stomach Mucosa	stomach
31	chr3:47204000-47207000	Active TSS	H9 Cell Line	embryonic stem cell
32	chr3:47204000-47207000	Active TSS	Aorta	Aorta
33	chr3:47204000-47207000	Active TSS	Fetal Stomach	stomach
34	chr3:47204000-47207200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:47204000-47207400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:47204000-47207400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:47204000-47207400	Active TSS	NHDF-Ad	bronchial
38	chr3:47204200-47205800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:47204200-47205800	Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr3:47204200-47205800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:47204200-47206400	Active TSS	Small Intestine	intestine
42	chr3:47204200-47206800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr3:47204200-47206800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:47204200-47206800	Active TSS	Fetal Muscle Trunk	muscle
45	chr3:47204200-47206800	Active TSS	Placenta Amnion	Placenta Amnion
46	chr3:47204200-47207000	Active TSS	Colonic Mucosa	Colon
47	chr3:47204200-47207000	Active TSS	Esophagus	oesophagus
48	chr3:47204200-47207000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr3:47204200-47207000	Active TSS	Placenta	Placenta
50	chr3:47204200-47207000	Active TSS	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links