Variant report

Variant	rs6544992
Chromosome Location	chr2:47715944-47715945
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	POLR2A	chr2:47715578-47717391	K562	blood:	n/a	n/a
2	POLR2A	chr2:47715883-47716670	MCF-7	breast:	n/a	n/a
3	FOSL2	chr2:47715943-47716622	SK-N-SH	brain:	n/a	n/a
4	GATA2	chr2:47715804-47716130	SH-SY5Y	brain:	n/a	n/a
5	MYC	chr2:47715901-47716496	MCF10A-Er-Src	breast:	n/a	chr2:47716133-47716142 chr2:47716131-47716141
6	MAX	chr2:47715822-47716582	A549	lung:	n/a	chr2:47716133-47716142 chr2:47716131-47716141
7	FOSL2	chr2:47715867-47716470	A549	lung:	n/a	n/a
8	TCF12	chr2:47715805-47716607	SK-N-SH	brain:	n/a	chr2:47716151-47716158
9	TCF12	chr2:47715896-47716501	A549	lung:	n/a	chr2:47716151-47716158
10	POLR2A	chr2:47715927-47716699	PANC-1	pancreas:	n/a	n/a
11	USF1	chr2:47715938-47716366	A549	lung:	n/a	n/a
12	USF1	chr2:47715926-47716392	A549	lung:	n/a	n/a
13	GATA3	chr2:47715742-47716305	MCF-7	breast:	n/a	n/a
14	POLR2A	chr2:47715755-47716800	H1-hESC	embryonic stem cell:	n/a	n/a
15	NFIC	chr2:47715879-47716633	SK-N-SH	brain:	n/a	n/a
16	GATA3	chr2:47715809-47716029	SH-SY5Y	brain:	n/a	n/a
17	JUND	chr2:47715847-47716542	SK-N-SH	brain:	n/a	n/a
18	MAX	chr2:47715918-47716375	MCF-7	breast:	n/a	chr2:47716133-47716142 chr2:47716131-47716141
19	MAX	chr2:47715886-47716506	A549	lung:	n/a	chr2:47716133-47716142 chr2:47716131-47716141
20	MAX	chr2:47715932-47716355	ECC-1	luminal epithelium:	n/a	chr2:47716133-47716142 chr2:47716131-47716141
21	GATA3	chr2:47715654-47716509	SK-N-SH	brain:	n/a	n/a
22	MAX	chr2:47715943-47716453	ECC-1	luminal epithelium:	n/a	chr2:47716133-47716142 chr2:47716131-47716141
23	POLR2A	chr2:47715840-47716330	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
ENSG00000236558	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10175959	0.81[ASN][1000 genomes]
rs10175972	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10179452	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10185866	0.92[CEU][hapmap];0.80[GIH][hapmap];0.91[TSI][hapmap]
rs10188090	0.82[ASN][1000 genomes]
rs10206575	0.90[EUR][1000 genomes]
rs10206782	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10209369	0.90[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs11684661	0.82[ASN][1000 genomes]
rs11684737	0.82[ASN][1000 genomes]
rs11886591	0.81[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs12991125	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13031342	0.89[EUR][1000 genomes]
rs1981928	0.92[EUR][1000 genomes]
rs2059520	0.84[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.82[ASN][1000 genomes]
rs3732182	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3732183	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3764959	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3764960	0.82[ASN][1000 genomes]
rs3771278	0.81[ASN][1000 genomes]
rs3771279	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3771280	0.95[GIH][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3821227	0.82[ASN][1000 genomes]
rs4550716	0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs4583514	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs6720549	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6720555	0.92[ASN][1000 genomes]
rs6722911	0.84[CHB][hapmap]
rs6725042	0.88[EUR][1000 genomes]
rs6726691	0.92[EUR][1000 genomes]
rs6737303	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6748435	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6757035	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6759990	0.90[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7584256	0.87[CEU][hapmap];0.88[TSI][hapmap]
rs7585174	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7588420	0.83[EUR][1000 genomes]
rs7596629	0.80[ASN][1000 genomes]
rs7607076	0.90[EUR][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	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv999576	chr2:47506116-47773960	Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6544992	MSH2	cis	Artery Tibial	GTEx
rs6544992	MSH2	cis	lung	GTEx

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47658200-47724800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:47658400-47716000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:47691600-47716000	Weak transcription	Gastric	stomach
4	chr2:47691600-47716000	Weak transcription	Pancreas	Pancrea
5	chr2:47693600-47716800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:47696000-47716000	Weak transcription	NHLF	lung
7	chr2:47696800-47716000	Weak transcription	Lung	lung
8	chr2:47697000-47716200	Weak transcription	Fetal Brain Female	brain
9	chr2:47702800-47727000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:47703800-47716000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:47703800-47722000	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:47704200-47716200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr2:47705800-47717000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:47706200-47716200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:47706600-47716200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:47708400-47716000	Weak transcription	HSMM	muscle
17	chr2:47710000-47716200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:47712000-47716000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:47712000-47716000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr2:47712000-47716200	Weak transcription	Fetal Stomach	stomach
21	chr2:47712200-47716400	Weak transcription	Fetal Intestine Large	intestine
22	chr2:47712200-47716400	Weak transcription	Left Ventricle	heart
23	chr2:47712600-47716000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr2:47712600-47716000	Weak transcription	Fetal Thymus	thymus
25	chr2:47712600-47716000	Weak transcription	Thymus	Thymus
26	chr2:47712600-47716400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr2:47712600-47716400	Weak transcription	Fetal Muscle Leg	muscle
28	chr2:47712600-47716600	Weak transcription	HepG2	liver
29	chr2:47712800-47716200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:47712800-47716400	Weak transcription	Hela-S3	cervix
31	chr2:47712800-47721800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr2:47713000-47716200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr2:47713000-47716200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:47713000-47716400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr2:47713000-47717400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:47713000-47717600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:47713200-47716400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr2:47713400-47716800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr2:47713600-47718200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:47714400-47716200	Enhancers	Stomach Mucosa	stomach
41	chr2:47714400-47717800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:47714600-47727200	Weak transcription	Primary T cells from cord blood	blood
43	chr2:47714800-47716000	Enhancers	A549	lung
44	chr2:47715000-47716000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr2:47715000-47716000	Weak transcription	Small Intestine	intestine
46	chr2:47715000-47716200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr2:47715000-47716400	Weak transcription	HSMMtube	muscle
48	chr2:47715000-47716800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:47715000-47717000	Weak transcription	Dnd41	blood
50	chr2:47715000-47721800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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