Variant report

Variant	rs10119641
Chromosome Location	chr9:110042247-110042248
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	STAT3	chr9:110042130-110042356	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr9:110042222-110042415	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:110022283..110024488-chr9:110040936..110043082,2	MCF-7	breast:
2	chr9:110014211..110018622-chr9:110040932..110043716,4	MCF-7	breast:
3	chr9:110034708..110043058-chr9:110043083..110050663,16	MCF-7	breast:

Variant related genes	Relation type
RAD23B	TF binding region
ENSG00000119318	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10113916	1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs10122970	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10481632	1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs10521083	0.84[CHB][hapmap]
rs10732368	0.84[CHB][hapmap]
rs10739232	0.88[CHB][hapmap]
rs10739234	0.84[CHB][hapmap];0.83[EUR][1000 genomes]
rs10739236	0.89[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs10739238	0.84[CHB][hapmap]
rs10759219	0.89[CHB][hapmap]
rs10759222	0.84[CHB][hapmap]
rs10816477	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs10816480	1.00[ASN][1000 genomes]
rs10816485	1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs10816490	0.88[ASN][1000 genomes]
rs10816491	0.88[ASN][1000 genomes]
rs10978767	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10978769	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs10978770	0.89[CHB][hapmap]
rs10978775	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10978776	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10978777	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10978791	1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs12342066	0.99[ASN][1000 genomes]
rs12345455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12555417	0.99[ASN][1000 genomes]
rs1323808	0.84[CHB][hapmap]
rs1535765	0.84[CHB][hapmap];0.80[EUR][1000 genomes]
rs1535766	0.89[CHB][hapmap]
rs1805329	1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs1805332	0.84[CHB][hapmap]
rs1805334	0.84[CHB][hapmap]
rs1886134	0.84[CHB][hapmap]
rs2005143	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2147071	0.80[EUR][1000 genomes]
rs2147072	0.84[CHB][hapmap]
rs2417776	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2417784	1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs2417785	0.84[CHB][hapmap]
rs28534368	0.90[ASN][1000 genomes]
rs28769087	0.97[ASN][1000 genomes]
rs28848858	0.99[ASN][1000 genomes]
rs4278207	0.84[CHB][hapmap]
rs4481670	0.83[CHB][hapmap]
rs4978844	0.81[EUR][1000 genomes]
rs4978849	0.83[CHB][hapmap]
rs61701375	0.93[ASN][1000 genomes]
rs698475	1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs7019341	0.81[EUR][1000 genomes]
rs7029997	0.84[CHB][hapmap];0.80[EUR][1000 genomes]
rs7030169	0.84[CHB][hapmap]
rs7030631	0.80[EUR][1000 genomes]
rs7031906	0.84[CHB][hapmap];0.80[EUR][1000 genomes]
rs7035611	0.84[CHB][hapmap];0.83[EUR][1000 genomes]
rs7036284	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7038737	0.83[CHB][hapmap];0.80[EUR][1000 genomes]
rs7039041	0.80[EUR][1000 genomes]
rs7040217	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7041137	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7041497	0.84[CHB][hapmap]
rs7043962	0.80[EUR][1000 genomes]
rs7046950	0.84[CHB][hapmap]
rs7852295	0.89[CHB][hapmap]
rs7856227	0.80[EUR][1000 genomes]
rs7866312	0.89[CHB][hapmap]
rs7866353	0.89[CHB][hapmap]
rs7866797	0.89[CHB][hapmap]
rs7867544	0.94[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs7873745	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs817836	1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs817838	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs817839	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs817840	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs817841	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs817843	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs817844	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs817845	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs817847	0.82[ASN][1000 genomes]
rs942291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs942293	0.84[CHB][hapmap]
rs9632893	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs9969728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv869351	chr9:109593212-110191170	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv530948	chr9:109760752-110413602	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv831682	chr9:109937181-110075453	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv893698	chr9:109998563-110052660	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv508560	chr9:110006490-110060539	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110035600-110044600	Enhancers	Placenta	Placenta
2	chr9:110036400-110044400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr9:110037800-110044000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:110038000-110043000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:110038000-110044400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr9:110038000-110044400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr9:110038000-110044400	Weak transcription	NH-A	brain
8	chr9:110038400-110043200	Weak transcription	GM12878-XiMat	blood
9	chr9:110039000-110042800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:110039000-110043000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr9:110039400-110042400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:110039600-110043400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr9:110039600-110044400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr9:110039800-110043200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:110039800-110044400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr9:110039800-110044400	Weak transcription	Adipose Nuclei	Adipose
17	chr9:110039800-110044400	Weak transcription	Colon Smooth Muscle	Colon
18	chr9:110039800-110044400	Weak transcription	A549	lung
19	chr9:110040000-110042800	Weak transcription	NHDF-Ad	bronchial
20	chr9:110040000-110042800	Weak transcription	Osteobl	bone
21	chr9:110040000-110044000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr9:110040200-110043000	Weak transcription	NHLF	lung
23	chr9:110040200-110044200	Weak transcription	HSMMtube	muscle
24	chr9:110040400-110043200	Weak transcription	Psoas Muscle	Psoas
25	chr9:110040400-110044000	Weak transcription	HSMM	muscle
26	chr9:110040400-110044200	Weak transcription	Fetal Heart	heart
27	chr9:110040400-110044200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr9:110040400-110044400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr9:110040400-110044400	Weak transcription	Fetal Muscle Leg	muscle
30	chr9:110040400-110044600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:110040400-110044600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr9:110040400-110044600	Weak transcription	Fetal Stomach	stomach
33	chr9:110040600-110043400	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr9:110042200-110042400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr9:110042200-110044400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr9:110042200-110044400	Enhancers	NHEK	skin
37	chr9:110042200-110044600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr9:110042200-110044600	Enhancers	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links