Variant report

Variant	rs13213175
Chromosome Location	chr6:5259868-5259869
allele	A/C
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	HCFC1	chr6:5259374-5262547	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr6:5259206-5262355	MCF10A-Er-Src	breast:	n/a	n/a
3	MYC	chr6:5259692-5261974	MCF10A-Er-Src	breast:	n/a	chr6:5261926-5261935 chr6:5261528-5261538 chr6:5259845-5259856 chr6:5261646-5261656
4	FOS	chr6:5259702-5259974	MCF10A-Er-Src	breast:	n/a	chr6:5259724-5259731
5	CEBPB	chr6:5259619-5259937	K562	blood:	n/a	n/a
6	MYC	chr6:5259671-5261955	MCF10A-Er-Src	breast:	n/a	chr6:5261926-5261935 chr6:5261528-5261538 chr6:5259845-5259856 chr6:5261646-5261656
7	STAT3	chr6:5259753-5259902	MCF10A-Er-Src	breast:	n/a	n/a
8	MXI1	chr6:5259637-5262620	IMR90	lung:	n/a	chr6:5261474-5261489
9	MAX	chr6:5259682-5260002	K562	blood:	n/a	chr6:5259845-5259856
10	STAT3	chr6:5259732-5259907	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr6:5259738-5259974	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr6:5259221-5262443	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5258576..5260130-chr6:5278247..5279774,2	K562	blood:
2	chr6:5230476..5232022-chr6:5258422..5260596,2	MCF-7	breast:

Variant related genes	Relation type
FARS2	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs13191522	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13197072	1.00[AMR][1000 genomes]
rs13199874	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13209775	1.00[AMR][1000 genomes]
rs13219725	1.00[AMR][1000 genomes]
rs34148454	1.00[AMR][1000 genomes]
rs34287447	1.00[AMR][1000 genomes]
rs34347613	1.00[AMR][1000 genomes]
rs34519114	1.00[AMR][1000 genomes]
rs34519637	1.00[AMR][1000 genomes]
rs34538064	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34774856	1.00[AMR][1000 genomes]
rs35100403	1.00[AMR][1000 genomes]
rs35237000	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35238319	1.00[AMR][1000 genomes]
rs35247793	1.00[AMR][1000 genomes]
rs35532313	1.00[AMR][1000 genomes]
rs35608724	1.00[AMR][1000 genomes]
rs36003115	1.00[AMR][1000 genomes]
rs71540851	1.00[AMR][1000 genomes]
rs71540854	1.00[AMR][1000 genomes]
rs71555880	1.00[AMR][1000 genomes]
rs71555881	1.00[AMR][1000 genomes]
rs71555884	1.00[AMR][1000 genomes]
rs71557548	1.00[AMR][1000 genomes]
rs71557555	1.00[AMR][1000 genomes]
rs71557557	1.00[AMR][1000 genomes]
rs9392660	1.00[AMR][1000 genomes]
rs9392661	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers 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 miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1034681	chr6:5070351-5387176	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv538113	chr6:5070351-5387176	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1018152	chr6:5077025-5387176	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv600873	chr6:5089278-5400658	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1030254	chr6:5132261-5431585	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers 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	10 gene(s)	inside rSNPs	diseases
9	nsv1034463	chr6:5137959-5345678	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers 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	10 gene(s)	inside rSNPs	diseases
10	nsv1021646	chr6:5157795-5367254	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv538115	chr6:5157795-5367254	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv1029609	chr6:5187633-5397254	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv1035080	chr6:5206533-5396019	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv538116	chr6:5206533-5396019	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv1016456	chr6:5216835-5315913	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS 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	8 gene(s)	inside rSNPs	diseases
16	nsv538117	chr6:5216835-5315913	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS 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	8 gene(s)	inside rSNPs	diseases
17	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
19	nsv522457	chr6:5245070-5260936	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv1028185	chr6:5247624-5340163	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5231000-5260200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr6:5231800-5260000	Weak transcription	NHLF	lung
3	chr6:5231800-5260200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:5232000-5260200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:5232400-5260000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:5236400-5260200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:5239000-5260200	Weak transcription	Colonic Mucosa	Colon
8	chr6:5240400-5260000	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr6:5241000-5260400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:5241400-5260200	Weak transcription	Fetal Kidney	kidney
11	chr6:5245200-5260000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr6:5247000-5260200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:5249000-5260200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:5249200-5260200	Weak transcription	Gastric	stomach
15	chr6:5250200-5260200	Weak transcription	HSMMtube	muscle
16	chr6:5252000-5260000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:5255400-5260400	Weak transcription	Aorta	Aorta
18	chr6:5258200-5260000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:5258600-5260000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr6:5258800-5260000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr6:5258800-5260200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr6:5259400-5260000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:5259400-5260000	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr6:5259400-5260000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:5259400-5260200	Enhancers	Primary T cells from cord blood	blood
26	chr6:5259400-5260200	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr6:5259400-5260200	Enhancers	Fetal Lung	lung
28	chr6:5259600-5260000	Enhancers	Primary hematopoietic stem cells	blood
29	chr6:5259600-5260000	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr6:5259600-5260000	Enhancers	Liver	Liver
31	chr6:5259600-5260000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr6:5259600-5260000	Enhancers	Fetal Intestine Large	intestine
33	chr6:5259600-5260000	Enhancers	Pancreatic Islets	Pancreatic Islet
34	chr6:5259600-5260000	Flanking Active TSS	K562	blood
35	chr6:5259600-5260200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr6:5259600-5260200	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr6:5259600-5260400	Enhancers	Spleen	Spleen
38	chr6:5259600-5260400	Flanking Active TSS	Hela-S3	cervix
39	chr6:5259600-5260400	Flanking Active TSS	HepG2	liver
40	chr6:5259600-5260600	Flanking Active TSS	Dnd41	blood
41	chr6:5259600-5263000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:5259600-5263200	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr6:5259800-5260000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
44	chr6:5259800-5260000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:5259800-5260000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr6:5259800-5260000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:5259800-5260000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr6:5259800-5260000	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr6:5259800-5260000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:5259800-5260000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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