Variant report

Variant	rs2143022
Chromosome Location	chr6:25316501-25316502
allele	A/C
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	chr6:25315748..25318380-chr6:25321578..25323806,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12055533	0.92[CEU][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12196702	0.83[ASN][1000 genomes]
rs1989206	0.98[ASN][1000 genomes]
rs2018839	0.80[CEU][hapmap]
rs2252012	0.91[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2328878	0.88[CEU][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2690109	0.94[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2690115	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2690120	0.87[CEU][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2690123	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2690125	0.92[CEU][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2690127	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2690129	0.92[CEU][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2690131	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2744290	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2744293	0.85[CEU][hapmap]
rs2744296	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2744299	1.00[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744302	0.92[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2744303	0.89[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4712908	0.84[ASN][1000 genomes]
rs9348670	0.97[ASN][1000 genomes]
rs9356973	0.97[ASN][1000 genomes]
rs9358850	0.92[CEU][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9358851	0.97[ASN][1000 genomes]
rs9379751	0.92[CEU][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9467465	0.81[CEU][hapmap];0.98[ASN][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	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

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25305000-25324400	Weak transcription	Left Ventricle	heart
2	chr6:25306600-25331400	Weak transcription	Spleen	Spleen
3	chr6:25310200-25316800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:25310400-25319400	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr6:25311600-25317200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:25311600-25317200	Enhancers	Fetal Lung	lung
7	chr6:25312000-25324200	Weak transcription	Esophagus	oesophagus
8	chr6:25312000-25324200	Weak transcription	Pancreas	Pancrea
9	chr6:25313400-25329800	Weak transcription	Primary T cells from cord blood	blood
10	chr6:25313600-25320200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:25313800-25318400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:25313800-25318400	Weak transcription	Lung	lung
13	chr6:25313800-25322800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr6:25313800-25325800	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr6:25313800-25326800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:25313800-25331400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr6:25314000-25318800	Weak transcription	Small Intestine	intestine
18	chr6:25314000-25325000	Weak transcription	Placenta	Placenta
19	chr6:25314200-25318400	Weak transcription	NHDF-Ad	bronchial
20	chr6:25314200-25319200	Weak transcription	Thymus	Thymus
21	chr6:25314600-25316800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:25314600-25317400	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr6:25314600-25317400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr6:25314800-25317400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:25314800-25317600	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr6:25314800-25319000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr6:25315000-25316600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:25315000-25316600	Enhancers	Brain Anterior Caudate	brain
29	chr6:25315000-25316600	Enhancers	Stomach Mucosa	stomach
30	chr6:25315000-25316800	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr6:25315400-25316800	Enhancers	Fetal Intestine Large	intestine
32	chr6:25315400-25329600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:25315600-25316600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:25315600-25316600	Enhancers	H9 Cell Line	embryonic stem cell
35	chr6:25315600-25316600	Enhancers	Duodenum Mucosa	Duodenum
36	chr6:25315600-25316600	Enhancers	Right Atrium	heart
37	chr6:25315600-25317200	Enhancers	Aorta	Aorta
38	chr6:25315800-25324200	Weak transcription	Hela-S3	cervix
39	chr6:25316000-25316600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr6:25316000-25316600	Enhancers	Ovary	ovary
41	chr6:25316000-25317000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr6:25316000-25317400	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr6:25316000-25320200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr6:25316000-25320400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr6:25316200-25316600	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr6:25316200-25318400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr6:25316200-25318400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr6:25316200-25319000	Weak transcription	Fetal Brain Female	brain
49	chr6:25316200-25319000	Weak transcription	Fetal Intestine Small	intestine
50	chr6:25316200-25320400	Weak transcription	Brain Cingulate Gyrus	brain

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