Variant report

Variant	rs9489491
Chromosome Location	chr6:118990620-118990621
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	GATA3	chr6:118989698-118990727	SK-N-SH	brain:	n/a	chr6:118990012-118990019 chr6:118990008-118990024 chr6:118990342-118990355 chr6:118990012-118990019 chr6:118990343-118990355 chr6:118990011-118990021 chr6:118990345-118990353 chr6:118990012-118990019 chr6:118990010-118990022
2	GATA3	chr6:118989815-118990825	MCF-7	breast:	n/a	chr6:118990012-118990019 chr6:118990008-118990024 chr6:118990342-118990355 chr6:118990012-118990019 chr6:118990343-118990355 chr6:118990011-118990021 chr6:118990345-118990353 chr6:118990012-118990019 chr6:118990010-118990022

No.	Distal block	Cell Line	Cell type
1	chr22:44769853..44770735-chr6:118990487..118991265,2	MCF-7	breast:
2	chr6:118985710..118987649-chr6:118989150..118991916,2	K562	blood:
3	chr6:118990170..118992293-chr6:119012694..119014681,2	K562	blood:
4	chr6:118988856..118991483-chr6:119002572..119005083,2	K562	blood:
5	chr6:118988812..118990874-chr6:118994587..118996786,2	K562	blood:
6	chr6:118989304..118991119-chr6:118993806..118996108,2	K562	blood:

Variant related genes	Relation type
CEP85L	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10081007	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12333080	1.00[YRI][hapmap]
rs13437605	1.00[YRI][hapmap]
rs17080292	1.00[YRI][hapmap]
rs17080302	0.92[YRI][hapmap]
rs17080456	0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs9320656	1.00[YRI][hapmap]
rs9320660	1.00[YRI][hapmap]
rs9481814	0.92[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9481820	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9481821	0.85[YRI][hapmap]
rs9481825	1.00[YRI][hapmap]
rs9481833	1.00[YRI][hapmap]
rs9481836	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9489407	1.00[YRI][hapmap]
rs9489409	1.00[YRI][hapmap]
rs9489413	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9489431	1.00[ASN][1000 genomes]
rs9489433	1.00[YRI][hapmap]
rs9489436	1.00[YRI][hapmap]
rs9489442	1.00[YRI][hapmap]
rs9489444	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9489447	1.00[YRI][hapmap]
rs9489452	1.00[YRI][hapmap]
rs9489457	1.00[YRI][hapmap]
rs9489458	1.00[YRI][hapmap]
rs9489460	1.00[YRI][hapmap]
rs9489462	1.00[YRI][hapmap]
rs9489466	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9489467	1.00[YRI][hapmap]
rs9489471	1.00[ASN][1000 genomes]
rs9489475	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489482	1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532051	chr6:118551027-119044197	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	9 gene(s)	inside rSNPs	diseases
2	nsv1020463	chr6:118593028-119146363	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1025403	chr6:118635123-119122551	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1025456	chr6:118669672-119058789	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1027444	chr6:118687556-119121660	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv538428	chr6:118687556-119121660	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv949321	chr6:118692304-119137658	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv432958	chr6:118692307-119010307	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv1034448	chr6:118698169-119016383	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv1025097	chr6:118699752-119058789	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
11	nsv532052	chr6:118711850-119057295	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	9 gene(s)	inside rSNPs	diseases
12	nsv432959	chr6:118716318-119010307	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
13	nsv604556	chr6:118722589-119065365	Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
14	nsv949416	chr6:118772508-119033063	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
15	nsv948980	chr6:118772508-119137658	Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
16	nsv604559	chr6:118786486-119113317	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
17	nsv1022865	chr6:118786586-119058789	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
18	nsv1020405	chr6:118786586-119241006	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118986400-118991400	Enhancers	Psoas Muscle	Psoas
2	chr6:118986400-118991800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:118986400-118992200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr6:118986400-118992400	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr6:118986400-118992400	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr6:118986400-118994800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr6:118986400-118995000	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr6:118986400-118995400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr6:118986400-119001800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:118986800-118990800	Weak transcription	Gastric	stomach
11	chr6:118987000-118993000	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr6:118988000-118991000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr6:118988000-118991000	Enhancers	Fetal Lung	lung
14	chr6:118988200-118991400	Enhancers	NHLF	lung
15	chr6:118988400-118990800	Enhancers	Muscle Satellite Cultured Cells	--
16	chr6:118988400-118991400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:118988800-118990800	Enhancers	NH-A	brain
18	chr6:118988800-118991000	Enhancers	Stomach Mucosa	stomach
19	chr6:118988800-118991000	Enhancers	HSMM	muscle
20	chr6:118988800-118991200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:118988800-118991200	Enhancers	Fetal Stomach	stomach
22	chr6:118988800-118991800	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr6:118989000-118991000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:118989200-118991200	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr6:118989200-118992600	Genic enhancers	Primary T cells from cord blood	blood
26	chr6:118989400-118991000	Enhancers	Adipose Nuclei	Adipose
27	chr6:118989400-118991200	Strong transcription	Primary B cells from cord blood	blood
28	chr6:118989400-118991400	Enhancers	Fetal Muscle Leg	muscle
29	chr6:118989400-118991800	Enhancers	Thymus	Thymus
30	chr6:118989600-118990800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:118989600-118991000	Enhancers	Fetal Kidney	kidney
32	chr6:118989600-118991000	Enhancers	Placenta	Placenta
33	chr6:118989600-118991400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr6:118989800-118991600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr6:118990000-118990800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:118990000-118991000	Flanking Active TSS	K562	blood
37	chr6:118990200-118991400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr6:118990400-118991200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr6:118990400-118991200	Enhancers	Fetal Thymus	thymus
40	chr6:118990400-119000200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr6:118990600-118991000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr6:118990600-118991200	Enhancers	HSMMtube	muscle
43	chr6:118990600-118992200	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr6:118990600-119025400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links