Variant report

Variant	rs9257345
Chromosome Location	chr6:28881064-28881065
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28874958..28881784-chr6:28883001..28892669,21	MCF-7	breast:
2	chr6:28872472..28877177-chr6:28878410..28882542,6	MCF-7	breast:
3	chr6:28833493..28835780-chr6:28880062..28881962,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212240	Chromatin interaction
ENSG00000204713	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs13206458	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3117146	0.85[EUR][1000 genomes]
rs3118357	0.89[EUR][1000 genomes]
rs3118359	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3118360	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3118361	0.92[EUR][1000 genomes]
rs3118364	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3118365	0.83[EUR][1000 genomes]
rs3118366	0.87[EUR][1000 genomes]
rs3118367	0.89[EUR][1000 genomes]
rs3129794	0.85[EUR][1000 genomes]
rs3129797	0.85[EUR][1000 genomes]
rs3129798	0.85[EUR][1000 genomes]
rs3130837	0.89[EUR][1000 genomes]
rs3130838	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3130844	0.92[EUR][1000 genomes]
rs3130845	0.92[EUR][1000 genomes]
rs3130846	0.89[EUR][1000 genomes]
rs3130847	0.92[EUR][1000 genomes]
rs3130885	0.94[EUR][1000 genomes]
rs3130887	0.87[EUR][1000 genomes]
rs3130888	0.85[EUR][1000 genomes]
rs3130891	0.85[EUR][1000 genomes]
rs3130892	0.92[EUR][1000 genomes]
rs3130893	0.85[EUR][1000 genomes]
rs3130894	0.85[EUR][1000 genomes]
rs3130895	0.91[EUR][1000 genomes]
rs3130896	0.85[EUR][1000 genomes]
rs3131068	0.92[EUR][1000 genomes]
rs3131069	0.92[EUR][1000 genomes]
rs3131071	0.92[EUR][1000 genomes]
rs3131072	0.92[EUR][1000 genomes]
rs3131073	0.89[EUR][1000 genomes]
rs3131075	0.92[EUR][1000 genomes]
rs3131076	0.92[EUR][1000 genomes]
rs3131081	0.85[EUR][1000 genomes]
rs3131085	0.81[EUR][1000 genomes]
rs3131093	0.87[EUR][1000 genomes]
rs3131094	0.89[EUR][1000 genomes]
rs3131095	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131096	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131097	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131101	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3131335	0.87[EUR][1000 genomes]
rs3131336	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131341	0.87[AMR][1000 genomes]
rs3131345	0.89[EUR][1000 genomes]
rs3132374	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3132376	0.89[EUR][1000 genomes]
rs3132378	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3132382	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132384	0.89[EUR][1000 genomes]
rs3132385	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3132387	0.87[EUR][1000 genomes]
rs3132388	0.89[EUR][1000 genomes]
rs3132389	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3132391	0.89[EUR][1000 genomes]
rs3132392	0.89[EUR][1000 genomes]
rs3132393	0.87[EUR][1000 genomes]
rs3132394	0.87[EUR][1000 genomes]
rs3132395	0.87[EUR][1000 genomes]
rs3135293	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3135295	0.89[EUR][1000 genomes]
rs3135297	0.90[EUR][1000 genomes]
rs3135298	0.87[EUR][1000 genomes]
rs3135299	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3135300	0.89[EUR][1000 genomes]
rs3135302	0.89[EUR][1000 genomes]
rs3135304	0.89[EUR][1000 genomes]
rs3135306	0.89[EUR][1000 genomes]
rs3135307	0.89[EUR][1000 genomes]
rs3135308	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3135309	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3135310	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3135311	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3135312	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3135313	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3135316	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3135317	0.85[EUR][1000 genomes]
rs3135318	0.92[EUR][1000 genomes]
rs3135325	0.92[EUR][1000 genomes]
rs7760313	0.87[EUR][1000 genomes]
rs9257140	0.87[AMR][1000 genomes]
rs9257167	0.87[AMR][1000 genomes]
rs9257245	0.87[EUR][1000 genomes]
rs9257249	0.92[EUR][1000 genomes]
rs9257250	0.92[EUR][1000 genomes]
rs9257262	0.89[EUR][1000 genomes]
rs9257267	0.85[EUR][1000 genomes]
rs9257272	0.89[EUR][1000 genomes]
rs9257331	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883518	chr6:28792477-28911802	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
3	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
4	nsv601212	chr6:28833225-28893927	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	nsv462667	chr6:28834646-28893927	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	nsv830622	chr6:28861667-29015804	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9257345	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs9257345	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs9257345	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28866000-28887000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:28867000-28889400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:28867600-28889200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:28867600-28889400	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr6:28867600-28889600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:28867800-28881600	Strong transcription	HSMM	muscle
7	chr6:28867800-28883200	Strong transcription	Muscle Satellite Cultured Cells	--
8	chr6:28867800-28885400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:28867800-28888200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:28867800-28888400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:28867800-28888400	Strong transcription	Fetal Thymus	thymus
12	chr6:28867800-28889200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:28867800-28889200	Strong transcription	HMEC	breast
14	chr6:28867800-28889400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:28867800-28889400	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:28867800-28889600	Strong transcription	Fetal Lung	lung
17	chr6:28868000-28889200	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr6:28868200-28887200	Strong transcription	HUVEC	blood vessel
19	chr6:28868200-28889600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr6:28868200-28889800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr6:28868400-28881600	Strong transcription	Stomach Smooth Muscle	stomach
22	chr6:28868400-28882600	Strong transcription	Liver	Liver
23	chr6:28868400-28884400	Strong transcription	Dnd41	blood
24	chr6:28868400-28886800	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr6:28868400-28887200	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr6:28868400-28888400	Strong transcription	Adipose Nuclei	Adipose
27	chr6:28868400-28888400	Strong transcription	Duodenum Mucosa	Duodenum
28	chr6:28868400-28888400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr6:28868400-28888400	Strong transcription	Fetal Brain Female	brain
30	chr6:28868400-28888400	Strong transcription	Fetal Muscle Leg	muscle
31	chr6:28868400-28888600	Strong transcription	Fetal Muscle Trunk	muscle
32	chr6:28868400-28889000	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:28868400-28889200	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr6:28868400-28889400	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr6:28868400-28889400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:28868600-28887200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr6:28868600-28887800	Strong transcription	Left Ventricle	heart
38	chr6:28868600-28888400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:28868600-28888600	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr6:28868600-28889400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr6:28868600-28889400	Strong transcription	Fetal Intestine Large	intestine
42	chr6:28868600-28889800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr6:28868800-28887200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr6:28869000-28882200	Strong transcription	Brain Angular Gyrus	brain
45	chr6:28869000-28885400	Strong transcription	HepG2	liver
46	chr6:28869000-28888600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:28869000-28889400	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr6:28869200-28886800	Strong transcription	Primary B cells from peripheral blood	blood
49	chr6:28869400-28884600	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr6:28869600-28889200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links