Variant report

Variant	rs7325962
Chromosome Location	chr13:49067103-49067104
allele	C/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	MYC	chr13:49066213-49067132	NB4	blood:	n/a	n/a
2	RELA	chr13:49066262-49067756	GM10847	blood:	n/a	n/a
3	POLR2A	chr13:49066488-49067116	HL-60	blood:	n/a	n/a
4	WRNIP1	chr13:49067074-49067244	GM12878	blood:	n/a	n/a
5	GATA1	chr13:49066497-49067256	PBDE	blood:	n/a	n/a
6	RELA	chr13:49065647-49067778	GM19099	blood:	n/a	n/a
7	POLR2A	chr13:49066396-49067129	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr13:49063049-49067797	GM12892	blood:	n/a	n/a
9	SPI1	chr13:49066081-49067106	HL-60	blood:	n/a	n/a
10	POLR2A	chr13:49066573-49067199	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr13:49065667-49067247	PBDE	blood:	n/a	n/a
12	POLR2A	chr13:49063878-49067866	GM19193	blood:	n/a	n/a
13	POLR2A	chr13:49066031-49067110	GM12878	blood:	n/a	n/a
14	RELA	chr13:49065483-49067807	GM15510	blood:	n/a	n/a
15	IRF4	chr13:49066517-49067110	GM12878	blood:	n/a	chr13:49066810-49066831
16	MTA3	chr13:49066009-49067680	GM12878	blood:	n/a	n/a
17	RELA	chr13:49066105-49067800	GM18951	blood:	n/a	n/a
18	POLR2A	chr13:49063103-49067843	GM12878	blood:	n/a	n/a
19	RCOR1	chr13:49066636-49067318	GM12878	blood:	n/a	n/a
20	IKZF1	chr13:49066198-49067298	GM12878	blood:	n/a	n/a
21	ATF2	chr13:49066426-49067129	GM12878	blood:	n/a	n/a
22	POLR2A	chr13:49066430-49067205	HL-60	blood:	n/a	n/a
23	POLR2A	chr13:49060366-49068321	GM12891	blood:	n/a	n/a
24	PAX5	chr13:49066219-49067156	GM12878	blood:	n/a	n/a
25	POLR2A	chr13:49063167-49068417	GM19099	blood:	n/a	n/a
26	POLR2A	chr13:49063104-49067911	GM18951	blood:	n/a	n/a
27	POLR2A	chr13:49062513-49068209	GM18505	blood:	n/a	n/a
28	SMC3	chr13:49066731-49067365	GM12878	blood:	n/a	n/a
29	RELA	chr13:49065544-49067468	GM18505	blood:	n/a	n/a
30	MAFK	chr13:49066974-49067139	HepG2	liver:	n/a	n/a
31	GATA2	chr13:49066294-49067212	HUVEC	blood vessel:	n/a	chr13:49066904-49066918
32	RELA	chr13:49066142-49067876	GM19193	blood:	n/a	n/a
33	BCLAF1	chr13:49066242-49067161	GM12878	blood:	n/a	n/a
34	REST	chr13:49066424-49067103	HL-60	blood:	n/a	n/a
35	NFIC	chr13:49066253-49067407	GM12878	blood:	n/a	n/a
36	MAX	chr13:49066196-49067229	NB4	blood:	n/a	n/a
37	FOXM1	chr13:49066204-49067233	GM12878	blood:	n/a	n/a
38	POLR2A	chr13:49064622-49067847	GM18526	blood:	n/a	n/a

Variant related genes	Relation type
RCBTB2	TF binding region

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1547660	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs171988	0.88[EUR][1000 genomes]
rs171990	0.88[EUR][1000 genomes]
rs174857	0.86[ASW][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs1926595	0.83[ASN][1000 genomes]
rs1926597	0.83[ASN][1000 genomes]
rs198564	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs198568	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs198571	0.86[ASW][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs198574	0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs198575	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs198576	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs198577	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs198606	0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs198608	0.81[EUR][1000 genomes]
rs198609	0.88[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes]
rs198610	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs198614	0.86[ASW][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs198622	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs198631	0.81[EUR][1000 genomes]
rs2070752	0.88[EUR][1000 genomes]
rs2274400	0.88[CHD][hapmap];0.90[JPT][hapmap]
rs2804094	0.90[JPT][hapmap];0.92[EUR][1000 genomes]
rs2804095	0.89[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes]
rs2854342	0.86[ASW][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs2854348	0.90[JPT][hapmap];0.92[EUR][1000 genomes]
rs2854353	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs2854357	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs2854362	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs3092888	0.88[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs3092898	0.87[ASN][1000 genomes]
rs3092899	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs3751380	0.87[ASW][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs398158	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs403390	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs406098	0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs4151434	0.90[JPT][hapmap]
rs4151442	0.89[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs4151448	0.89[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs4151452	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs4151456	0.80[JPT][hapmap]
rs4151474	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs4151525	0.90[JPT][hapmap]
rs4151601	0.88[CHD][hapmap];0.90[JPT][hapmap]
rs425834	0.89[CHB][hapmap];0.88[EUR][1000 genomes]
rs427686	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs449268	0.91[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes]
rs61074776	0.83[ASN][1000 genomes]
rs6561448	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6561457	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6561461	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs7326934	0.91[AMR][1000 genomes]
rs7329039	0.83[ASN][1000 genomes]
rs7329865	0.90[JPT][hapmap]
rs73486867	0.83[ASN][1000 genomes]
rs73495016	0.87[ASN][1000 genomes]
rs7985825	0.83[ASN][1000 genomes]
rs7992129	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7995216	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs7996186	0.90[JPT][hapmap]
rs7996402	0.83[ASN][1000 genomes]
rs7998781	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs8001241	1.00[ASW][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs8002565	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9316385	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9316386	0.82[MEX][hapmap];0.85[TSI][hapmap]
rs9316396	1.00[TSI][hapmap]
rs9316401	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9331965	0.88[CHD][hapmap];0.90[JPT][hapmap]
rs9331973	0.90[JPT][hapmap]
rs9332054	0.88[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9591172	0.83[ASN][1000 genomes]
rs9591177	0.81[ASN][1000 genomes]
rs9591178	0.83[ASN][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	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	esv3384312	chr13:49063851-49067249	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49023800-49073800	Weak transcription	NH-A	brain
2	chr13:49028000-49071000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr13:49030600-49070600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr13:49032400-49067400	Weak transcription	Pancreas	Pancrea
5	chr13:49032400-49067600	Weak transcription	Gastric	stomach
6	chr13:49034400-49073800	Weak transcription	Esophagus	oesophagus
7	chr13:49035200-49073400	Weak transcription	Fetal Intestine Small	intestine
8	chr13:49053600-49071200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr13:49054000-49094000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr13:49057400-49068400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr13:49060600-49067400	Weak transcription	Stomach Mucosa	stomach
12	chr13:49061400-49072000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr13:49062400-49067200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
14	chr13:49062600-49070800	Weak transcription	Fetal Brain Male	brain
15	chr13:49062800-49067400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr13:49062800-49070400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr13:49062800-49072000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr13:49063000-49067400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr13:49063000-49068000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr13:49063000-49087800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr13:49063200-49067400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr13:49063200-49071000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr13:49063600-49067200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr13:49063600-49067600	Weak transcription	Brain Germinal Matrix	brain
25	chr13:49064000-49067200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
26	chr13:49064000-49067200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr13:49064200-49068200	Flanking Active TSS	GM12878-XiMat	blood
28	chr13:49064200-49069800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr13:49064200-49075200	Weak transcription	Fetal Intestine Large	intestine
30	chr13:49064400-49068000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr13:49064400-49068800	Flanking Active TSS	Dnd41	blood
32	chr13:49064600-49070600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr13:49064800-49067200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr13:49064800-49067200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr13:49064800-49071200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr13:49065000-49067200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
37	chr13:49065000-49067200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr13:49065000-49069800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr13:49065000-49070200	Weak transcription	Fetal Muscle Trunk	muscle
40	chr13:49065400-49067200	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr13:49065400-49067400	Flanking Active TSS	NHDF-Ad	bronchial
42	chr13:49065400-49069400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr13:49065400-49072000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr13:49065600-49067200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr13:49065600-49067200	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr13:49065600-49067200	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr13:49065600-49067200	Active TSS	Right Atrium	heart
48	chr13:49065600-49067400	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr13:49065600-49069000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr13:49065800-49067200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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