Variant report

Variant	rs3131072
Chromosome Location	chr6:28919896-28919897
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28863784..28865629-chr6:28918637..28921778,3	MCF-7	breast:
2	chr6:28807797..28809537-chr6:28919515..28922301,2	K562	blood:
3	chr6:28918185..28920512-chr6:28921430..28924835,3	MCF-7	breast:
4	chr6:28918865..28920559-chr6:28953984..28955919,2	MCF-7	breast:
5	chr6:28829833..28833248-chr6:28918976..28922184,3	K562	blood:
6	chr6:28916972..28925607-chr6:28947207..28951909,14	K562	blood:
7	chr6:28905933..28927444-chr6:28943937..28954526,53	K562	blood:
8	chr6:28806197..28808344-chr6:28919521..28922266,2	MCF-7	breast:
9	chr6:28919130..28921907-chr6:28978530..28981244,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000225173	Chromatin interaction
ENSG00000225595	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000263426	Chromatin interaction
ENSG00000227214	Chromatin interaction
ENSG00000244349	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1233618	0.80[EUR][1000 genomes]
rs1233620	0.80[EUR][1000 genomes]
rs1233623	0.80[EUR][1000 genomes]
rs13206458	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3117146	0.92[EUR][1000 genomes]
rs3118357	0.96[EUR][1000 genomes]
rs3118359	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3118360	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3118361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3118364	0.91[EUR][1000 genomes]
rs3118365	0.91[EUR][1000 genomes]
rs3118366	0.94[EUR][1000 genomes]
rs3118367	0.96[EUR][1000 genomes]
rs3129791	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3129794	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3129797	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3129798	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3130777	1.00[AFR][1000 genomes]
rs3130837	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130838	0.96[EUR][1000 genomes]
rs3130844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130845	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3130847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130885	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3130887	0.94[EUR][1000 genomes]
rs3130888	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3130890	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3130891	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3130892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130893	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3130894	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3130895	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3130896	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3131068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131069	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131073	0.96[EUR][1000 genomes]
rs3131075	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131076	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131081	0.92[EUR][1000 genomes]
rs3131085	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3131093	0.94[EUR][1000 genomes]
rs3131094	0.96[EUR][1000 genomes]
rs3131095	0.96[EUR][1000 genomes]
rs3131096	0.96[EUR][1000 genomes]
rs3131097	0.96[EUR][1000 genomes]
rs3131101	0.96[EUR][1000 genomes]
rs3131335	0.94[EUR][1000 genomes]
rs3131336	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3131340	0.85[EUR][1000 genomes]
rs3131341	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3131343	0.84[EUR][1000 genomes]
rs3131345	0.96[EUR][1000 genomes]
rs3132373	0.84[EUR][1000 genomes]
rs3132374	0.93[EUR][1000 genomes]
rs3132376	0.96[EUR][1000 genomes]
rs3132378	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3132382	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3132384	0.96[EUR][1000 genomes]
rs3132385	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3132387	0.94[EUR][1000 genomes]
rs3132388	0.96[EUR][1000 genomes]
rs3132389	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3132391	0.96[EUR][1000 genomes]
rs3132392	0.96[EUR][1000 genomes]
rs3132393	0.94[EUR][1000 genomes]
rs3132394	0.94[EUR][1000 genomes]
rs3132395	0.94[EUR][1000 genomes]
rs3132396	0.85[EUR][1000 genomes]
rs3135293	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3135294	0.84[EUR][1000 genomes]
rs3135295	0.96[EUR][1000 genomes]
rs3135297	0.91[EUR][1000 genomes]
rs3135298	0.94[EUR][1000 genomes]
rs3135299	0.92[EUR][1000 genomes]
rs3135300	0.96[EUR][1000 genomes]
rs3135302	0.96[EUR][1000 genomes]
rs3135304	0.96[EUR][1000 genomes]
rs3135306	0.96[EUR][1000 genomes]
rs3135307	0.96[EUR][1000 genomes]
rs3135308	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3135309	0.96[EUR][1000 genomes]
rs3135310	0.96[EUR][1000 genomes]
rs3135311	0.96[EUR][1000 genomes]
rs3135312	0.96[EUR][1000 genomes]
rs3135313	0.96[EUR][1000 genomes]
rs3135316	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3135317	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3135318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135325	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4324798	0.85[EUR][1000 genomes]
rs7760313	0.94[EUR][1000 genomes]
rs7761321	0.84[EUR][1000 genomes]
rs7766699	0.80[EUR][1000 genomes]
rs7767099	0.84[EUR][1000 genomes]
rs9257167	0.80[EUR][1000 genomes]
rs9257183	0.80[EUR][1000 genomes]
rs9257184	0.80[EUR][1000 genomes]
rs9257187	0.80[EUR][1000 genomes]
rs9257188	0.80[EUR][1000 genomes]
rs9257189	0.80[EUR][1000 genomes]
rs9257192	0.80[EUR][1000 genomes]
rs9257217	0.84[EUR][1000 genomes]
rs9257223	0.85[EUR][1000 genomes]
rs9257227	0.82[EUR][1000 genomes]
rs9257245	0.94[EUR][1000 genomes]
rs9257249	0.92[EUR][1000 genomes]
rs9257250	0.92[EUR][1000 genomes]
rs9257262	0.96[EUR][1000 genomes]
rs9257267	0.93[EUR][1000 genomes]
rs9257272	0.96[EUR][1000 genomes]
rs9257331	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs9257345	0.92[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3131072	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs3131072	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs3131072	ZFP57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 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	chr6:28912400-28920800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr6:28912400-28921200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:28912400-28921200	Weak transcription	Fetal Intestine Small	intestine
5	chr6:28912400-28921200	Weak transcription	Right Atrium	heart
6	chr6:28915600-28921200	Weak transcription	Esophagus	oesophagus
7	chr6:28915800-28920600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:28916000-28920800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr6:28916000-28921200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:28916200-28920800	Weak transcription	NH-A	brain
11	chr6:28916200-28920800	Weak transcription	Osteobl	bone
12	chr6:28916200-28921200	Weak transcription	HMEC	breast
13	chr6:28916200-28921200	Weak transcription	NHEK	skin
14	chr6:28916400-28921200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:28916600-28920600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:28916800-28921200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:28917000-28920800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:28917000-28921200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:28918600-28921200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:28918800-28920800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr6:28918800-28920800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr6:28918800-28921000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:28919000-28921000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:28919200-28920000	Enhancers	K562	blood
25	chr6:28919200-28920600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr6:28919200-28920800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr6:28919200-28920800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr6:28919200-28920800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr6:28919200-28921200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr6:28919400-28920200	Weak transcription	Hela-S3	cervix
31	chr6:28919600-28920200	Weak transcription	A549	lung
32	chr6:28919800-28920200	Active TSS	HepG2	liver
33	chr6:28919800-28921200	Weak transcription	Placenta	Placenta

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