Variant report

Variant	rs58191968
Chromosome Location	chr6:25314138-25314139
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	chr6:25314031..25316618-chr6:25318937..25320645,2	MCF-7	breast:
2	chr6:25278102..25281759-chr6:25312379..25314512,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079691	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs12055697	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs16890366	0.97[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1883393	0.92[ASN][1000 genomes]
rs2143023	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2690042	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2744287	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4712904	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4712905	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4712906	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4712907	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55967593	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs55999195	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60084615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456664	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6456665	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6456666	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6456668	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6903148	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6906812	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6913606	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6913886	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6914439	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6914514	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6914654	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6914798	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6914930	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6915270	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6917631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921343	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6923529	0.95[ASN][1000 genomes]
rs6927238	0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6938281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs730711	0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs73392399	0.95[ASN][1000 genomes]
rs73396126	0.89[ASN][1000 genomes]
rs7741580	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7743750	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7746942	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7746969	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7755701	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7756143	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7758529	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7759796	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7759879	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7760067	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7760151	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7764111	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9295654	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9348671	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9356974	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9366616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9366617	0.82[AFR][1000 genomes]
rs9379752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9379753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9393639	0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9461132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9461134	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9461135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9461136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9467466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs999039	0.95[AFR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv16338	chr6:25312436-25315638	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25303200-25314800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr6:25303400-25315400	Weak transcription	Fetal Kidney	kidney
3	chr6:25305000-25324400	Weak transcription	Left Ventricle	heart
4	chr6:25306600-25331400	Weak transcription	Spleen	Spleen
5	chr6:25310200-25314200	Enhancers	Fetal Intestine Small	intestine
6	chr6:25310200-25316800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:25310400-25319400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr6:25310800-25315000	Weak transcription	Brain Anterior Caudate	brain
9	chr6:25311400-25314400	Enhancers	Osteobl	bone
10	chr6:25311600-25314200	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr6:25311600-25314200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:25311600-25314400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr6:25311600-25315400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:25311600-25317200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:25311600-25317200	Enhancers	Fetal Lung	lung
16	chr6:25312000-25314200	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr6:25312000-25315600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr6:25312000-25315600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:25312000-25324200	Weak transcription	Esophagus	oesophagus
20	chr6:25312000-25324200	Weak transcription	Pancreas	Pancrea
21	chr6:25312200-25315600	Weak transcription	Right Atrium	heart
22	chr6:25312200-25316000	Weak transcription	Gastric	stomach
23	chr6:25312400-25314200	Enhancers	Thymus	Thymus
24	chr6:25312600-25315600	Weak transcription	Fetal Thymus	thymus
25	chr6:25313400-25314200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:25313400-25314200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:25313400-25314200	Enhancers	Ovary	ovary
28	chr6:25313400-25314200	Enhancers	HMEC	breast
29	chr6:25313400-25315400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr6:25313400-25315400	Weak transcription	Fetal Heart	heart
31	chr6:25313400-25329800	Weak transcription	Primary T cells from cord blood	blood
32	chr6:25313600-25314200	Enhancers	Muscle Satellite Cultured Cells	--
33	chr6:25313600-25314200	Enhancers	NHDF-Ad	bronchial
34	chr6:25313600-25314200	Enhancers	NHLF	lung
35	chr6:25313600-25314400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:25313600-25315200	Enhancers	HSMMtube	muscle
37	chr6:25313600-25315400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:25313600-25316200	Enhancers	Fetal Brain Male	brain
39	chr6:25313600-25320200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:25313800-25314400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:25313800-25314400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:25313800-25314800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:25313800-25314800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr6:25313800-25314800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr6:25313800-25314800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr6:25313800-25314800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr6:25313800-25315000	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr6:25313800-25315000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:25313800-25315000	Weak transcription	Stomach Mucosa	stomach
50	chr6:25313800-25315000	Enhancers	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links