Variant report

Variant	rs10245036
Chromosome Location	chr7:86847321-86847322
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	chr7:86847053-86850217	GM12891	blood:	n/a	n/a
2	POLR2A	chr7:86847159-86847949	GM12892	blood:	n/a	n/a
3	MAX	chr7:86847292-86850397	GM12878	blood:	n/a	chr7:86849135-86849144 chr7:86850066-86850076 chr7:86849873-86849883 chr7:86849400-86849410
4	MTA3	chr7:86845490-86850382	GM12878	blood:	n/a	n/a
5	MXI1	chr7:86845672-86850248	GM12878	blood:	n/a	chr7:86850067-86850076
6	EBF1	chr7:86847261-86847354	GM12878	blood:	n/a	n/a
7	RELA	chr7:86847292-86850571	GM18951	blood:	n/a	n/a
8	POLR2A	chr7:86845591-86850232	GM12878	blood:	n/a	n/a
9	NFIC	chr7:86847122-86847891	GM12878	blood:	n/a	chr7:86847797-86847814
10	POLR2A	chr7:86847209-86847622	GM12878	blood:	n/a	n/a
11	POLR2A	chr7:86845415-86850229	GM12892	blood:	n/a	n/a
12	POLR2A	chr7:86845510-86850220	GM12892	blood:	n/a	n/a
13	POLR2A	chr7:86845609-86847456	GM15510	blood:	n/a	n/a
14	ZNF263	chr7:86847246-86847689	HEK293-T-REx	kidney:	n/a	n/a
15	PML	chr7:86845395-86850265	GM12878	blood:	n/a	n/a
16	POLR2A	chr7:86845697-86847586	GM12878	blood:	n/a	n/a
17	POLR2A	chr7:86845478-86850122	GM12878	blood:	n/a	n/a
18	POLR2A	chr7:86846992-86847753	GM12891	blood:	n/a	n/a
19	RELA	chr7:86847165-86850542	GM10847	blood:	n/a	n/a
20	POLR2A	chr7:86847024-86847910	GM12891	blood:	n/a	n/a
21	CHD1	chr7:86845583-86850123	GM12878	blood:	n/a	chr7:86849182-86849192 chr7:86849216-86849226 chr7:86849405-86849415
22	NFATC1	chr7:86845501-86847579	GM12878	blood:	n/a	n/a
23	POLR2A	chr7:86845624-86847662	GM12878	blood:	n/a	n/a
24	POLR2A	chr7:86847226-86847488	GM12878	blood:	n/a	n/a
25	POLR2A	chr7:86845561-86850194	GM19099	blood:	n/a	n/a
26	POLR2A	chr7:86847302-86847382	GM12878	blood:	n/a	n/a
27	RELA	chr7:86847253-86850532	GM12891	blood:	n/a	n/a
28	POLR2A	chr7:86845580-86850213	GM19193	blood:	n/a	n/a
29	TBP	chr7:86847157-86848482	GM12878	blood:	n/a	n/a
30	CEBPB	chr7:86845493-86847383	GM12878	blood:	n/a	n/a
31	POLR2A	chr7:86845478-86850208	GM12878	blood:	n/a	n/a
32	RELA	chr7:86845597-86850332	GM15510	blood:	n/a	n/a
33	POLR2A	chr7:86845576-86850266	GM12891	blood:	n/a	n/a
34	POLR2A	chr7:86847156-86847516	GM12891	blood:	n/a	n/a
35	POLR2A	chr7:86845407-86850212	GM12892	blood:	n/a	n/a
36	POLR2A	chr7:86845568-86850200	GM18505	blood:	n/a	n/a
37	RELA	chr7:86847157-86849410	GM19099	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:86846140..86849007-chr7:86974665..86976624,2	MCF-7	breast:
2	chr7:86780355..86788679-chr7:86845137..86851399,15	MCF-7	breast:
3	chr7:86778653..86785496-chr7:86845746..86851349,11	MCF-7	breast:
4	chr7:86823088..86825610-chr7:86847212..86850126,2	MCF-7	breast:
5	chr6:108881430..108882088-chr7:86846802..86847370,2	Hela-S3	cervix:
6	chr2:20648875..20651258-chr7:86847173..86848866,2	MCF-7	breast:
7	chr7:86547065..86549255-chr7:86847292..86849668,2	MCF-7	breast:
8	chr7:86822309..86824785-chr7:86846167..86848975,3	MCF-7	breast:

Variant related genes	Relation type
TMEM243	TF binding region
ENSG00000224046	Chromatin interaction
ENSG00000228950	Chromatin interaction
ENSG00000135164	Chromatin interaction
ENSG00000182165	Chromatin interaction
ENSG00000164659	Chromatin interaction
ENSG00000005469	Chromatin interaction
ENSG00000118689	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1011952	0.88[EUR][1000 genomes]
rs1011953	0.89[EUR][1000 genomes]
rs10263920	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10273826	0.94[CEU][hapmap];0.91[CHB][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1058972	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1558050	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1574795	0.94[CEU][hapmap];0.81[CHB][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2074757	0.82[GIH][hapmap]
rs2106955	0.89[EUR][1000 genomes]
rs2108272	0.82[GIH][hapmap]
rs2190424	0.86[GIH][hapmap]
rs2286267	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2286268	0.86[GIH][hapmap]
rs3747807	0.82[GIH][hapmap]
rs3789251	0.82[GIH][hapmap]
rs3810883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4236504	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs4728685	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4728686	0.82[GIH][hapmap]
rs4728688	0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs4728690	0.87[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6465099	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6465100	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6942878	0.90[EUR][1000 genomes]
rs6952842	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6957785	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6966613	0.95[JPT][hapmap]
rs6975175	0.95[EUR][1000 genomes]
rs6978590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs757159	1.00[CEU][hapmap];0.84[JPT][hapmap];0.90[EUR][1000 genomes]
rs769156	1.00[CEU][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs7776634	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7792031	0.81[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7793356	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7800541	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7810647	0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025277	chr7:86299224-87206007	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv538999	chr7:86299224-87206007	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv532147	chr7:86299225-87121975	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	nsv1016761	chr7:86758544-86914152	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv888676	chr7:86781423-86858824	Active TSS Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Enhancers 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	57 gene(s)	inside rSNPs	diseases
6	nsv1026193	chr7:86790391-86856448	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS 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
7	nsv539003	chr7:86790391-86856448	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS 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
8	nsv888677	chr7:86802025-87781111	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv464622	chr7:86832603-87541248	Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
10	nsv607725	chr7:86832603-87541248	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10245036	C7orf23	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:86821000-86847400	Weak transcription	Stomach Mucosa	stomach
2	chr7:86825600-86847400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr7:86826800-86848200	Weak transcription	Left Ventricle	heart
4	chr7:86828400-86848200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr7:86829800-86848000	Weak transcription	Right Ventricle	heart
6	chr7:86834600-86847400	Weak transcription	Esophagus	oesophagus
7	chr7:86834600-86848200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr7:86836200-86847400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr7:86836400-86848000	Weak transcription	A549	lung
10	chr7:86836600-86847800	Weak transcription	NH-A	brain
11	chr7:86837400-86847800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr7:86837400-86848200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr7:86837400-86848200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr7:86838200-86847800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr7:86838400-86848000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr7:86839200-86848000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr7:86839600-86848200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr7:86840800-86848000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr7:86841400-86848000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr7:86841600-86848000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr7:86841800-86848000	Weak transcription	HSMMtube	muscle
22	chr7:86842600-86847400	Weak transcription	Placenta	Placenta
23	chr7:86842600-86847400	Weak transcription	Right Atrium	heart
24	chr7:86843600-86847400	Weak transcription	Ovary	ovary
25	chr7:86843600-86847800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr7:86843600-86848000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr7:86843800-86847400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr7:86844200-86847600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr7:86844200-86847600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr7:86844800-86847400	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr7:86844800-86847400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr7:86844800-86848200	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr7:86845000-86847400	Enhancers	Small Intestine	intestine
34	chr7:86845200-86848400	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr7:86845200-86848400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr7:86845400-86850200	Active TSS	GM12878-XiMat	blood
37	chr7:86845600-86847400	Enhancers	Pancreas	Pancrea
38	chr7:86845600-86847600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr7:86845600-86847600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
40	chr7:86845600-86847800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr7:86845600-86848200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr7:86845600-86848200	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr7:86845600-86848400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr7:86845800-86847400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr7:86845800-86847400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr7:86845800-86847600	Weak transcription	Liver	Liver
47	chr7:86845800-86848200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr7:86845800-86848200	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr7:86846000-86847600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr7:86846000-86847600	Enhancers	HepG2	liver

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