Variant report

Variant	rs17139776
Chromosome Location	chr6:5208529-5208530
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5203877..5206736-chr6:5207600..5210343,2	MCF-7	breast:

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10485195	1.00[AMR][1000 genomes]
rs11242997	1.00[ASN][1000 genomes]
rs11242998	1.00[ASN][1000 genomes]
rs13197147	0.83[AMR][1000 genomes]
rs13202971	1.00[ASN][1000 genomes]
rs13213703	1.00[ASN][1000 genomes]
rs13217077	1.00[ASN][1000 genomes]
rs13219584	1.00[ASN][1000 genomes]
rs13219950	1.00[ASN][1000 genomes]
rs17133271	1.00[ASN][1000 genomes]
rs17139710	1.00[AMR][1000 genomes]
rs17139780	0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs17139831	1.00[ASN][1000 genomes]
rs17139838	1.00[ASN][1000 genomes]
rs17139841	1.00[ASN][1000 genomes]
rs17139846	1.00[ASN][1000 genomes]
rs17139848	1.00[ASN][1000 genomes]
rs17139851	1.00[ASN][1000 genomes]
rs17139853	1.00[ASN][1000 genomes]
rs17139856	1.00[ASN][1000 genomes]
rs17139860	1.00[ASN][1000 genomes]
rs17139926	0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs17139944	0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs17140032	0.83[YRI][hapmap]
rs34041880	1.00[ASN][1000 genomes]
rs34110180	1.00[ASN][1000 genomes]
rs34120947	1.00[ASN][1000 genomes]
rs34146318	1.00[ASN][1000 genomes]
rs34170037	1.00[ASN][1000 genomes]
rs34211615	1.00[ASN][1000 genomes]
rs34265509	1.00[ASN][1000 genomes]
rs34421021	1.00[ASN][1000 genomes]
rs34449449	1.00[ASN][1000 genomes]
rs34512910	1.00[ASN][1000 genomes]
rs34711553	1.00[ASN][1000 genomes]
rs34713043	1.00[ASN][1000 genomes]
rs34786730	1.00[ASN][1000 genomes]
rs34903116	1.00[ASN][1000 genomes]
rs34908251	1.00[ASN][1000 genomes]
rs34968006	1.00[ASN][1000 genomes]
rs34968842	1.00[ASN][1000 genomes]
rs35039476	1.00[ASN][1000 genomes]
rs35073344	1.00[ASN][1000 genomes]
rs35218696	1.00[ASN][1000 genomes]
rs35277899	1.00[ASN][1000 genomes]
rs35372007	1.00[ASN][1000 genomes]
rs35525232	1.00[ASN][1000 genomes]
rs35570153	1.00[AMR][1000 genomes]
rs35587351	1.00[ASN][1000 genomes]
rs35656919	1.00[ASN][1000 genomes]
rs35864979	1.00[ASN][1000 genomes]
rs35972876	1.00[ASN][1000 genomes]
rs36007403	1.00[ASN][1000 genomes]
rs56034435	1.00[ASN][1000 genomes]
rs58508775	1.00[ASN][1000 genomes]
rs59994371	1.00[ASN][1000 genomes]
rs60489951	1.00[ASN][1000 genomes]
rs60890075	1.00[ASN][1000 genomes]
rs61089858	1.00[ASN][1000 genomes]
rs62385015	1.00[ASN][1000 genomes]
rs6901286	1.00[ASN][1000 genomes]
rs6921627	1.00[ASN][1000 genomes]
rs6935667	1.00[ASN][1000 genomes]
rs6935687	1.00[ASN][1000 genomes]
rs71555883	1.00[ASN][1000 genomes]
rs71555885	1.00[ASN][1000 genomes]
rs71555886	1.00[ASN][1000 genomes]
rs71557546	1.00[ASN][1000 genomes]
rs71557549	1.00[ASN][1000 genomes]
rs71557550	1.00[ASN][1000 genomes]
rs71557551	1.00[ASN][1000 genomes]
rs73365051	1.00[ASN][1000 genomes]
rs73365064	1.00[ASN][1000 genomes]
rs73365082	1.00[ASN][1000 genomes]
rs73719720	1.00[ASN][1000 genomes]
rs73719741	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv1017821	chr6:5114609-5213200	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
9	nsv538114	chr6:5114609-5213200	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	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
14	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
15	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
16	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

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5176200-5239600	Weak transcription	Thymus	Thymus
2	chr6:5180200-5212200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr6:5182000-5213600	Weak transcription	Gastric	stomach
4	chr6:5189000-5213200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr6:5192800-5213000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:5193200-5212400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:5194000-5220800	Weak transcription	GM12878-XiMat	blood
8	chr6:5201200-5208800	Enhancers	Fetal Muscle Leg	muscle
9	chr6:5201600-5213400	Weak transcription	Fetal Brain Male	brain
10	chr6:5201800-5213400	Weak transcription	Fetal Brain Female	brain
11	chr6:5202000-5212800	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr6:5202800-5213600	Weak transcription	Dnd41	blood
13	chr6:5203200-5210000	Enhancers	Fetal Stomach	stomach
14	chr6:5203400-5208600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:5203600-5210400	Enhancers	Colon Smooth Muscle	Colon
16	chr6:5203800-5209000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:5203800-5213400	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr6:5204000-5208600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:5204200-5208600	Enhancers	Fetal Kidney	kidney
20	chr6:5204200-5209400	Enhancers	Rectal Smooth Muscle	rectum
21	chr6:5204400-5208600	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr6:5204400-5213000	Weak transcription	Hela-S3	cervix
23	chr6:5204600-5208800	Enhancers	Brain Angular Gyrus	brain
24	chr6:5204800-5208800	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr6:5205200-5208600	Enhancers	Aorta	Aorta
26	chr6:5205600-5212200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:5205600-5213000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr6:5205600-5213400	Weak transcription	Fetal Thymus	thymus
29	chr6:5205600-5218800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr6:5205600-5220000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr6:5205600-5223000	Weak transcription	Right Atrium	heart
32	chr6:5205800-5208600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr6:5206200-5214800	Weak transcription	Esophagus	oesophagus
34	chr6:5206200-5215600	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr6:5206200-5215600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr6:5206200-5246800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr6:5206400-5212600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr6:5206400-5213400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr6:5206400-5214000	Weak transcription	Spleen	Spleen
40	chr6:5206400-5219400	Weak transcription	HMEC	breast
41	chr6:5206600-5208600	Enhancers	Stomach Smooth Muscle	stomach
42	chr6:5206600-5211800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr6:5206600-5212400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr6:5206600-5212800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:5206600-5213000	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr6:5206600-5213000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:5206600-5213200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr6:5206600-5213200	Weak transcription	Brain Germinal Matrix	brain
49	chr6:5206600-5213600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr6:5206600-5213600	Weak transcription	A549	lung

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