Variant report

Variant	rs3130896
Chromosome Location	chr6:28983887-28983888
allele	A/G/T
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28831141..28836054-chr6:28982378..28987476,7	MCF-7	breast:
2	chr6:28971200..28973323-chr6:28982235..28984571,2	MCF-7	breast:
3	chr6:28983036..28984978-chr6:28993896..28995733,2	K562	blood:
4	chr6:28801618..28804388-chr6:28983054..28984845,2	MCF-7	breast:
5	chr6:28978104..28979854-chr6:28982165..28984128,2	K562	blood:
6	chr6:28892042..28894995-chr6:28981382..28984107,2	K562	blood:
7	chr6:28889593..28893449-chr6:28983117..28986574,5	K562	blood:
8	chr6:28889755..28892054-chr6:28980985..28986161,5	MCF-7	breast:
9	chr6:28861653..28865693-chr6:28983461..28986677,4	K562	blood:
10	chr6:28916735..28919060-chr6:28983575..28986159,2	K562	blood:
11	chr6:28890021..28893121-chr6:28982575..28985723,3	MCF-7	breast:
12	chr6:28910912..28914377-chr6:28983886..28986579,4	K562	blood:
13	chr6:28946686..28952098-chr6:28981757..28987491,9	K562	blood:
14	chr6:28956424..28958160-chr6:28982849..28984604,2	K562	blood:
15	chr6:28888057..28891991-chr6:28982896..28986559,7	K562	blood:
16	chr6:28804930..28806893-chr6:28983119..28985051,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000225595	Chromatin interaction
ENSG00000223677	Chromatin interaction
ENSG00000204709	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000225173	Chromatin interaction
ENSG00000197935	Chromatin interaction
ENSG00000204713	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs13206458	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3117146	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3117337	0.87[AMR][1000 genomes]
rs3117339	0.87[AMR][1000 genomes]
rs3117342	0.89[AMR][1000 genomes];0.80[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];0.92[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]
rs3129104	0.87[AMR][1000 genomes]
rs3129120	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3129791	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3129794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3129797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3129798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130777	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3130808	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3130820	0.89[AMR][1000 genomes]
rs3130828	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3130831	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3130837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3130838	0.96[EUR][1000 genomes]
rs3130844	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3130845	0.92[EUR][1000 genomes]
rs3130846	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3130847	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3130885	0.91[EUR][1000 genomes]
rs3130887	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3130888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130890	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3130891	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130892	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3130893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130895	0.91[EUR][1000 genomes]
rs3131068	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3131069	0.92[EUR][1000 genomes]
rs3131071	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3131072	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3131073	0.89[EUR][1000 genomes]
rs3131075	0.92[EUR][1000 genomes]
rs3131076	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3131081	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131085	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[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	0.89[EUR][1000 genomes]
rs3131335	0.94[EUR][1000 genomes]
rs3131336	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3131345	0.96[EUR][1000 genomes]
rs3132374	0.93[EUR][1000 genomes]
rs3132376	0.96[EUR][1000 genomes]
rs3132378	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3132382	1.00[AFR][1000 genomes];0.92[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]
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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135318	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3135325	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4947263	0.80[EUR][1000 genomes]
rs7760313	0.94[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	0.85[EUR][1000 genomes]
rs9257611	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1023540	chr6:28922691-29326018	Active TSS Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
4	nsv538169	chr6:28922691-29326018	Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv869541	chr6:28922692-29326017	Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv916439	chr6:28922697-29326087	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv462668	chr6:28922719-29342775	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
8	nsv601213	chr6:28922719-29342775	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
9	nsv1015796	chr6:28923980-29342825	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
10	nsv462669	chr6:28936556-29337500	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
11	nsv601214	chr6:28936556-29337500	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
12	nsv601215	chr6:28946920-29348297	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
13	nsv1023028	chr6:28956136-29343575	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
14	nsv538170	chr6:28956136-29343575	ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
15	nsv1018937	chr6:28956136-29366175	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
16	nsv1032468	chr6:28968930-29155749	Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
17	nsv1026403	chr6:28981639-29343575	Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
18	nsv538171	chr6:28981639-29343575	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3130896	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs3130896	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs3130896	ZFP57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28979600-28984000	Weak transcription	Right Atrium	heart
2	chr6:28979600-28984200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:28982200-28984400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:28982200-28985200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr6:28982200-28985200	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr6:28982400-28984000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:28982600-28984000	ZNF genes & repeats	Spleen	Spleen
8	chr6:28982800-28984000	Active TSS	HMEC	breast
9	chr6:28982800-28984600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:28982800-28985200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:28983000-28984200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:28983200-28984000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:28983200-28984000	Weak transcription	Osteobl	bone
14	chr6:28983200-28985200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:28983400-28984000	Weak transcription	Gastric	stomach
16	chr6:28983400-28984000	Weak transcription	Lung	lung
17	chr6:28983400-28984000	Active TSS	Ovary	ovary
18	chr6:28983400-28984200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:28983600-28984000	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:28983600-28984200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
21	chr6:28983600-28984200	Bivalent/Poised TSS	Esophagus	oesophagus
22	chr6:28983800-28984000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
23	chr6:28983800-28984000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
24	chr6:28983800-28984000	Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr6:28983800-28984000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:28983800-28984000	Bivalent/Poised TSS	Primary T helper naive cells from peripheral blood	blood
27	chr6:28983800-28984000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:28983800-28984000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
29	chr6:28983800-28984000	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
30	chr6:28983800-28984000	Active TSS	Liver	Liver
31	chr6:28983800-28984000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
32	chr6:28983800-28984000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
33	chr6:28983800-28984000	Bivalent Enhancer	Fetal Thymus	thymus
34	chr6:28983800-28984000	Enhancers	Pancreas	Pancrea
35	chr6:28983800-28984000	Active TSS	Rectal Mucosa Donor 31	rectum
36	chr6:28983800-28984000	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
37	chr6:28983800-28984000	Bivalent Enhancer	Thymus	Thymus
38	chr6:28983800-28984000	Enhancers	NH-A	brain
39	chr6:28983800-28984200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
40	chr6:28983800-28984200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
41	chr6:28983800-28984200	Active TSS	Duodenum Mucosa	Duodenum
42	chr6:28983800-28984200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
43	chr6:28983800-28984200	Enhancers	Placenta Amnion	Placenta Amnion
44	chr6:28983800-28984200	Active TSS	Rectal Smooth Muscle	rectum
45	chr6:28983800-28984200	ZNF genes & repeats	GM12878-XiMat	blood
46	chr6:28983800-28984200	Flanking Bivalent TSS/Enh	HepG2	liver
47	chr6:28983800-28984400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
48	chr6:28983800-28984400	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
49	chr6:28983800-28984400	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
50	chr6:28983800-28984400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood

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