Variant report

Variant	rs9489484
Chromosome Location	chr6:118970950-118970951
allele	G/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	MXI1	chr6:118970121-118973661	SK-N-SH	brain:	n/a	chr6:118973072-118973081
2	EBF1	chr6:118970560-118970982	GM12878	blood:	n/a	chr6:118970774-118970787 chr6:118970776-118970785 chr6:118970774-118970785

No.	Distal block	Cell Line	Cell type
1	chr6:118957671..118960010-chr6:118969497..118972042,2	MCF-7	breast:
2	chr6:118970545..118972377-chr6:119033430..119035366,2	K562	blood:
3	chr6:118957533..118960044-chr6:118968927..118971676,4	K562	blood:
4	chr6:118962546..118964256-chr6:118970270..118972608,2	MCF-7	breast:
5	chr6:118969568..118974185-chr6:119029207..119033276,8	K562	blood:
6	chr6:118969208..118971248-chr6:118973177..118975161,3	K562	blood:

Variant related genes	Relation type
CEP85L	TF binding region
ENSG00000111860	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10080340	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10155773	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10214801	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10457339	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10457340	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10457346	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11153749	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11153762	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12190964	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12191005	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12191529	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12191962	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12192532	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12197348	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12199189	1.00[AMR][1000 genomes]
rs12199190	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12200660	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12201928	1.00[EUR][1000 genomes]
rs12202466	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12202932	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12204374	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12205793	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12206369	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12206459	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12207554	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12209500	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12209566	0.83[AMR][1000 genomes]
rs12211934	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12212089	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12213494	1.00[EUR][1000 genomes]
rs12215364	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12215456	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12215565	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12215706	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13328242	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13437148	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13437314	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60500545	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6903291	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6903632	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6904070	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6904344	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6934770	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6939873	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7743702	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7755203	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7759420	1.00[AMR][1000 genomes]
rs7764014	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9320657	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9320659	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9320661	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9320662	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9372510	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9387582	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9398488	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9481812	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9481818	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9481822	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9481823	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9481824	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9481829	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9481830	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9481835	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9481839	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9489398	0.88[AFR][1000 genomes]
rs9489402	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9489408	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9489410	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9489415	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9489422	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9489427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9489430	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9489434	0.92[AFR][1000 genomes]
rs9489435	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9489451	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9489464	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9489468	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9489472	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9489480	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9489481	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9489485	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9489488	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9489490	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9489492	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9489495	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9489496	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9489501	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9489505	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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
19	nsv1030331	chr6:118874345-118975680	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118953200-118971400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr6:118953800-118971200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr6:118965600-118971200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:118966600-118971200	Weak transcription	Right Ventricle	heart
5	chr6:118966800-118971200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:118966800-118971200	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr6:118966800-118971200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:118966800-118971400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:118966800-118971400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:118966800-118971400	Weak transcription	Left Ventricle	heart
11	chr6:118966800-118971400	Weak transcription	Pancreas	Pancrea
12	chr6:118967400-118971200	Weak transcription	Fetal Thymus	thymus
13	chr6:118967400-118971400	Weak transcription	Aorta	Aorta
14	chr6:118969400-118971400	Weak transcription	Gastric	stomach
15	chr6:118970000-118971200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:118970000-118973000	Active TSS	GM12878-XiMat	blood
17	chr6:118970000-118973200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:118970000-118973200	Active TSS	Fetal Brain Male	brain
19	chr6:118970200-118971600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:118970200-118971600	Flanking Active TSS	HUVEC	blood vessel
21	chr6:118970200-118973000	Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr6:118970200-118973000	Active TSS	HMEC	breast
23	chr6:118970200-118973200	Active TSS	NHLF	lung
24	chr6:118970400-118971000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:118970400-118971000	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr6:118970400-118971000	Enhancers	Primary T cells from cord blood	blood
27	chr6:118970400-118971000	Enhancers	Primary hematopoietic stem cells	blood
28	chr6:118970400-118971000	Enhancers	Liver	Liver
29	chr6:118970400-118971000	Flanking Active TSS	Brain Angular Gyrus	brain
30	chr6:118970400-118971000	Flanking Active TSS	Fetal Brain Female	brain
31	chr6:118970400-118971000	Enhancers	Rectal Smooth Muscle	rectum
32	chr6:118970400-118971200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:118970400-118971200	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr6:118970400-118971200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr6:118970400-118971200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr6:118970400-118971200	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr6:118970400-118971200	Enhancers	Adipose Nuclei	Adipose
38	chr6:118970400-118971200	Enhancers	Brain Hippocampus Middle	brain
39	chr6:118970400-118971200	Enhancers	Colon Smooth Muscle	Colon
40	chr6:118970400-118971200	Enhancers	Fetal Heart	heart
41	chr6:118970400-118971200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr6:118970400-118971200	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr6:118970400-118971200	Flanking Active TSS	Osteobl	bone
44	chr6:118970400-118971400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr6:118970400-118971400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr6:118970400-118971400	Flanking Active TSS	Brain Substantia Nigra	brain
47	chr6:118970400-118971600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:118970400-118971600	Flanking Active TSS	Brain Anterior Caudate	brain
49	chr6:118970400-118971600	Bivalent/Poised TSS	Fetal Lung	lung
50	chr6:118970400-118971600	Flanking Active TSS	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links