Variant report

Variant	rs10399993
Chromosome Location	chr10:98747753-98747754
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	MAFK	chr10:98746756-98747973	IMR90	lung:	n/a	chr10:98746882-98746893 chr10:98746880-98746894 chr10:98747451-98747467 chr10:98747451-98747466 chr10:98746881-98746896 chr10:98747452-98747472 chr10:98746909-98746924 chr10:98747456-98747466 chr10:98746881-98746892 chr10:98747451-98747462 chr10:98746882-98746893 chr10:98747456-98747465 chr10:98746881-98746892
2	POLR2A	chr10:98747692-98747909	HepG2	liver:	n/a	n/a
3	POLR2A	chr10:98747646-98748743	K562	blood:	n/a	n/a
4	POLR2A	chr10:98747746-98747871	GM12878	blood:	n/a	n/a
5	MAFF	chr10:98747304-98747771	K562	blood:	n/a	chr10:98747449-98747467 chr10:98747455-98747469

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:98741127..98743717-chr10:98745929..98748788,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231025	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10882853	0.81[ASN][1000 genomes]
rs10882854	0.86[ASW][hapmap];0.83[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.81[ASN][1000 genomes]
rs10882857	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11188985	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2185294	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.90[TSI][hapmap]
rs2225344	0.81[ASN][1000 genomes]
rs3814162	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4532970	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4542327	0.81[ASN][1000 genomes]
rs4919056	0.81[ASN][1000 genomes]
rs4919058	0.86[ASW][hapmap];0.83[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.81[ASN][1000 genomes]
rs4919060	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4919061	0.91[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7069290	0.86[ASW][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.81[ASN][1000 genomes]
rs7080839	0.86[ASW][hapmap];0.83[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7894160	0.93[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7912176	0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs9702665	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1052931	chr10:98676192-98862301	Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1042398	chr10:98691406-98851346	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv831951	chr10:98717103-98761280	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98734000-98748400	Weak transcription	Stomach Mucosa	stomach
2	chr10:98741200-98747800	Weak transcription	Psoas Muscle	Psoas
3	chr10:98741200-98758000	Weak transcription	K562	blood
4	chr10:98741600-98750600	Weak transcription	NHEK	skin
5	chr10:98741600-98751400	Weak transcription	Small Intestine	intestine
6	chr10:98741800-98748000	Weak transcription	Colon Smooth Muscle	Colon
7	chr10:98742000-98748000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr10:98742000-98757000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr10:98742200-98747800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr10:98742200-98748200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr10:98742200-98748200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr10:98742200-98750800	Weak transcription	HMEC	breast
13	chr10:98742200-98752200	Weak transcription	Colonic Mucosa	Colon
14	chr10:98742200-98754600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr10:98742200-98754600	Weak transcription	Right Ventricle	heart
16	chr10:98742200-98754800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr10:98742200-98755000	Weak transcription	Left Ventricle	heart
18	chr10:98742400-98747800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr10:98742400-98748000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr10:98742400-98748000	Weak transcription	Fetal Kidney	kidney
21	chr10:98742400-98750200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr10:98742400-98750200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr10:98742400-98751200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr10:98742400-98751400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr10:98742400-98752400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr10:98742600-98748200	Weak transcription	Aorta	Aorta
27	chr10:98742600-98748400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr10:98742600-98750800	Weak transcription	A549	lung
29	chr10:98742600-98752600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr10:98742600-98752800	Weak transcription	Gastric	stomach
31	chr10:98742600-98755800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr10:98742600-98756000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr10:98742600-98756800	Weak transcription	Lung	lung
34	chr10:98743000-98748000	Weak transcription	Fetal Lung	lung
35	chr10:98743000-98758600	Weak transcription	Spleen	Spleen
36	chr10:98743200-98749200	Weak transcription	HepG2	liver
37	chr10:98743400-98747800	Weak transcription	NH-A	brain
38	chr10:98743600-98750400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr10:98743600-98750400	Weak transcription	Fetal Intestine Large	intestine
40	chr10:98743800-98758000	Weak transcription	Fetal Brain Female	brain
41	chr10:98744000-98748200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr10:98744400-98752200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr10:98744600-98750400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr10:98744600-98751000	Weak transcription	Fetal Intestine Small	intestine
45	chr10:98745000-98747800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr10:98745000-98749000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr10:98745000-98758400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr10:98745200-98756000	Weak transcription	Fetal Muscle Trunk	muscle
49	chr10:98745200-98760400	Weak transcription	Primary T cells from cord blood	blood
50	chr10:98745400-98748200	Weak transcription	Fetal Stomach	stomach

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