Variant report

Variant	rs3131073
Chromosome Location	chr6:28920972-28920973
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28863784..28865629-chr6:28918637..28921778,3	MCF-7	breast:
2	chr6:28910397..28912982-chr6:28920133..28921972,2	MCF-7	breast:
3	chr6:28807797..28809537-chr6:28919515..28922301,2	K562	blood:
4	chr6:28863727..28866430-chr6:28920617..28922633,3	K562	blood:
5	chr6:28920218..28924369-chr6:28968578..28972504,4	K562	blood:
6	chr6:28920183..28922796-chr6:28965172..28967810,2	K562	blood:
7	chr6:28857766..28860290-chr6:28920868..28922677,2	K562	blood:
8	chr22:29197206..29200027-chr6:28920726..28923051,2	MCF-7	breast:
9	chr6:28907315..28909915-chr6:28920300..28923261,2	MCF-7	breast:
10	chr6:28829833..28833248-chr6:28918976..28922184,3	K562	blood:
11	chr6:28889277..28892149-chr6:28920165..28923545,3	K562	blood:
12	chr6:28916972..28925607-chr6:28947207..28951909,14	K562	blood:
13	chr6:28905933..28927444-chr6:28943937..28954526,53	K562	blood:
14	chr6:28806197..28808344-chr6:28919521..28922266,2	MCF-7	breast:
15	chr6:28919130..28921907-chr6:28978530..28981244,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000263426	Chromatin interaction
ENSG00000204709	Chromatin interaction
ENSG00000225173	Chromatin interaction
ENSG00000227214	Chromatin interaction
ENSG00000225595	Chromatin interaction
ENSG00000226471	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000224157	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs13206458	0.96[EUR][1000 genomes]
rs3117146	0.89[EUR][1000 genomes]
rs3118357	0.93[EUR][1000 genomes]
rs3118359	0.93[EUR][1000 genomes]
rs3118360	0.85[EUR][1000 genomes]
rs3118361	0.96[EUR][1000 genomes]
rs3118364	0.87[EUR][1000 genomes]
rs3118365	0.87[EUR][1000 genomes]
rs3118366	0.91[EUR][1000 genomes]
rs3118367	0.93[EUR][1000 genomes]
rs3129791	0.82[EUR][1000 genomes]
rs3129794	0.89[EUR][1000 genomes]
rs3129797	0.89[EUR][1000 genomes]
rs3129798	0.89[EUR][1000 genomes]
rs3130837	0.93[EUR][1000 genomes]
rs3130838	0.93[EUR][1000 genomes]
rs3130844	0.96[EUR][1000 genomes]
rs3130845	0.96[EUR][1000 genomes]
rs3130846	0.93[EUR][1000 genomes]
rs3130847	0.96[EUR][1000 genomes]
rs3130885	0.94[EUR][1000 genomes]
rs3130887	0.91[EUR][1000 genomes]
rs3130888	0.89[EUR][1000 genomes]
rs3130891	0.89[EUR][1000 genomes]
rs3130892	0.96[EUR][1000 genomes]
rs3130893	0.89[EUR][1000 genomes]
rs3130894	0.89[EUR][1000 genomes]
rs3130895	0.94[EUR][1000 genomes]
rs3130896	0.89[EUR][1000 genomes]
rs3131068	0.96[EUR][1000 genomes]
rs3131069	0.96[EUR][1000 genomes]
rs3131071	0.96[EUR][1000 genomes]
rs3131072	0.96[EUR][1000 genomes]
rs3131075	0.96[EUR][1000 genomes]
rs3131076	0.96[EUR][1000 genomes]
rs3131081	0.89[EUR][1000 genomes]
rs3131085	0.85[EUR][1000 genomes]
rs3131093	0.91[EUR][1000 genomes]
rs3131094	0.93[EUR][1000 genomes]
rs3131095	0.93[EUR][1000 genomes]
rs3131096	0.93[EUR][1000 genomes]
rs3131097	0.93[EUR][1000 genomes]
rs3131101	0.93[EUR][1000 genomes]
rs3131335	0.91[EUR][1000 genomes]
rs3131336	0.93[EUR][1000 genomes]
rs3131340	0.82[EUR][1000 genomes]
rs3131341	0.82[EUR][1000 genomes]
rs3131343	0.80[EUR][1000 genomes]
rs3131345	0.93[EUR][1000 genomes]
rs3132373	0.80[EUR][1000 genomes]
rs3132374	0.89[EUR][1000 genomes]
rs3132376	0.93[EUR][1000 genomes]
rs3132378	0.93[EUR][1000 genomes]
rs3132382	0.96[EUR][1000 genomes]
rs3132384	0.93[EUR][1000 genomes]
rs3132385	0.93[EUR][1000 genomes]
rs3132387	0.91[EUR][1000 genomes]
rs3132388	0.93[EUR][1000 genomes]
rs3132389	0.93[EUR][1000 genomes]
rs3132391	0.93[EUR][1000 genomes]
rs3132392	0.93[EUR][1000 genomes]
rs3132393	0.91[EUR][1000 genomes]
rs3132394	0.91[EUR][1000 genomes]
rs3132395	0.91[EUR][1000 genomes]
rs3132396	0.82[EUR][1000 genomes]
rs3135293	0.93[EUR][1000 genomes]
rs3135294	0.80[EUR][1000 genomes]
rs3135295	0.93[EUR][1000 genomes]
rs3135297	0.87[EUR][1000 genomes]
rs3135298	0.91[EUR][1000 genomes]
rs3135299	0.89[EUR][1000 genomes]
rs3135300	0.93[EUR][1000 genomes]
rs3135302	0.93[EUR][1000 genomes]
rs3135304	0.93[EUR][1000 genomes]
rs3135306	0.93[EUR][1000 genomes]
rs3135307	0.93[EUR][1000 genomes]
rs3135308	0.93[EUR][1000 genomes]
rs3135309	0.93[EUR][1000 genomes]
rs3135310	0.93[EUR][1000 genomes]
rs3135311	0.93[EUR][1000 genomes]
rs3135312	0.93[EUR][1000 genomes]
rs3135313	0.93[EUR][1000 genomes]
rs3135316	0.93[EUR][1000 genomes]
rs3135317	0.89[EUR][1000 genomes]
rs3135318	0.96[EUR][1000 genomes]
rs3135325	0.96[EUR][1000 genomes]
rs4324798	0.82[EUR][1000 genomes]
rs7760313	0.91[EUR][1000 genomes]
rs7761321	0.80[EUR][1000 genomes]
rs7767099	0.80[EUR][1000 genomes]
rs9257217	0.80[EUR][1000 genomes]
rs9257223	0.82[EUR][1000 genomes]
rs9257245	0.91[EUR][1000 genomes]
rs9257249	0.89[EUR][1000 genomes]
rs9257250	0.89[EUR][1000 genomes]
rs9257262	0.93[EUR][1000 genomes]
rs9257267	0.89[EUR][1000 genomes]
rs9257272	0.93[EUR][1000 genomes]
rs9257331	0.93[EUR][1000 genomes]
rs9257345	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	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
2	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
3	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3131073	BTN3A2	trans	lymphoblastoid	seeQTL
rs3131073	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs3131073	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs3131073	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28912200-28921200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:28912400-28921200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:28912400-28921200	Weak transcription	Fetal Intestine Small	intestine
4	chr6:28912400-28921200	Weak transcription	Right Atrium	heart
5	chr6:28915600-28921200	Weak transcription	Esophagus	oesophagus
6	chr6:28916000-28921200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:28916200-28921200	Weak transcription	HMEC	breast
8	chr6:28916200-28921200	Weak transcription	NHEK	skin
9	chr6:28916400-28921200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr6:28916800-28921200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:28917000-28921200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr6:28918600-28921200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:28918800-28921000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:28919000-28921000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:28919200-28921200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr6:28919800-28921200	Weak transcription	Placenta	Placenta
17	chr6:28920000-28921000	Flanking Active TSS	K562	blood
18	chr6:28920200-28921000	Flanking Active TSS	HepG2	liver
19	chr6:28920200-28922200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:28920400-28921200	Weak transcription	Right Ventricle	heart
21	chr6:28920600-28921600	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr6:28920600-28922200	Active TSS	H9 Cell Line	embryonic stem cell
23	chr6:28920600-28922400	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr6:28920800-28921000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr6:28920800-28921000	Flanking Active TSS	Hela-S3	cervix
26	chr6:28920800-28921200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:28920800-28921200	Enhancers	Primary T cells fromperipheralblood	blood
28	chr6:28920800-28921200	Enhancers	Muscle Satellite Cultured Cells	--
29	chr6:28920800-28921200	Enhancers	NH-A	brain
30	chr6:28920800-28921200	Enhancers	Osteobl	bone
31	chr6:28920800-28921400	Active TSS	H1 Cell Line	embryonic stem cell
32	chr6:28920800-28921400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:28920800-28921400	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr6:28920800-28921400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:28920800-28921400	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr6:28920800-28921600	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr6:28920800-28921600	Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr6:28920800-28921600	Active TSS	Fetal Kidney	kidney
39	chr6:28920800-28921800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr6:28920800-28922200	Active TSS	GM12878-XiMat	blood
41	chr6:28920800-28922400	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr6:28920800-28922400	Active TSS	A549	lung
43	chr6:28920800-28922400	Active TSS	NHDF-Ad	bronchial

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