Variant report

Variant	rs257971
Chromosome Location	chr5:118839707-118839708
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:118831350..118835449-chr5:118835713..118839843,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133835	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs161852	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2257900	0.97[ASN][1000 genomes]
rs2259347	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2451816	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs246965	0.85[ASN][1000 genomes]
rs246967	0.85[ASN][1000 genomes]
rs2546210	0.84[ASN][1000 genomes]
rs25640	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs257970	0.99[ASN][1000 genomes]
rs257972	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs257973	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs257974	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs257975	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs257978	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2678070	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2678091	0.99[ASN][1000 genomes]
rs2945327	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs32651	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs32659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs32662	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs32663	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs32665	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35235684	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3850202	0.85[ASN][1000 genomes]
rs39971	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs457106	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs463098	0.83[ASN][1000 genomes]
rs463513	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427732	chr5:118730999-119034741	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1024455	chr5:118770429-119487982	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS 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	13 gene(s)	inside rSNPs	diseases
3	nsv1016271	chr5:118836891-119487982	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118791800-118846600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:118794800-118861200	Weak transcription	HSMM	muscle
3	chr5:118804200-118879600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr5:118806000-118846400	Weak transcription	Esophagus	oesophagus
5	chr5:118806000-118846400	Weak transcription	Spleen	Spleen
6	chr5:118806200-118844800	Weak transcription	Thymus	Thymus
7	chr5:118806200-118846400	Weak transcription	Pancreas	Pancrea
8	chr5:118806200-118855600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:118806400-118845000	Weak transcription	Fetal Stomach	stomach
10	chr5:118806400-118846400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:118806800-118845400	Weak transcription	Fetal Heart	heart
12	chr5:118808000-118839800	Weak transcription	Psoas Muscle	Psoas
13	chr5:118812000-118846400	Weak transcription	NHLF	lung
14	chr5:118814000-118845000	Weak transcription	Gastric	stomach
15	chr5:118814000-118845200	Weak transcription	Aorta	Aorta
16	chr5:118814800-118844800	Weak transcription	Lung	lung
17	chr5:118815800-118845400	Weak transcription	HMEC	breast
18	chr5:118816000-118844000	Weak transcription	Hela-S3	cervix
19	chr5:118816000-118847000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr5:118817000-118846400	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr5:118819600-118844400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr5:118820200-118846400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr5:118821000-118843800	Weak transcription	NHDF-Ad	bronchial
24	chr5:118827600-118847800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr5:118828000-118840400	Weak transcription	Osteobl	bone
26	chr5:118829200-118840200	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr5:118829800-118844800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr5:118830400-118845200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr5:118831000-118840200	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr5:118832400-118878200	Weak transcription	NH-A	brain
31	chr5:118832600-118844400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr5:118832600-118868600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr5:118832800-118843800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr5:118832800-118844600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr5:118833000-118840800	Weak transcription	Fetal Muscle Trunk	muscle
36	chr5:118833000-118841200	Weak transcription	HSMMtube	muscle
37	chr5:118833000-118860200	Weak transcription	Stomach Mucosa	stomach
38	chr5:118833200-118840200	Weak transcription	A549	lung
39	chr5:118833200-118845000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr5:118833200-118845000	Weak transcription	Ovary	ovary
41	chr5:118833200-118845000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr5:118833200-118846000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr5:118834400-118847800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr5:118834800-118846400	Weak transcription	Small Intestine	intestine
45	chr5:118835400-118840000	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr5:118835800-118839800	Weak transcription	Brain Hippocampus Middle	brain
47	chr5:118836000-118839800	Weak transcription	Brain Angular Gyrus	brain
48	chr5:118836000-118844800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr5:118836000-118844800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr5:118836000-118850600	Weak transcription	HUVEC	blood vessel

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