Variant report

Variant	rs3135308
Chromosome Location	chr6:28852156-28852157
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28851004..28853039-chr6:28863239..28865119,3	MCF-7	breast:
2	chr6:28851984..28853619-chr6:28890283..28892430,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224157	Chromatin interaction
ENSG00000204713	Chromatin interaction

Extended variants
information (count: 136 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs1233579	0.80[EUR][1000 genomes]
rs1233580	0.80[EUR][1000 genomes]
rs1233581	0.80[EUR][1000 genomes]
rs1233583	0.80[EUR][1000 genomes]
rs1233593	0.80[EUR][1000 genomes]
rs1233594	0.80[EUR][1000 genomes]
rs1233599	0.84[EUR][1000 genomes]
rs1233600	0.84[EUR][1000 genomes]
rs1233604	0.84[EUR][1000 genomes]
rs1233618	0.84[EUR][1000 genomes]
rs1233620	0.84[EUR][1000 genomes]
rs1233623	0.84[EUR][1000 genomes]
rs1238262	0.80[EUR][1000 genomes]
rs1311912	0.80[EUR][1000 genomes]
rs1311913	0.80[EUR][1000 genomes]
rs13206458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13217472	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs3117146	0.96[EUR][1000 genomes]
rs3118357	1.00[EUR][1000 genomes]
rs3118359	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3118360	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3118361	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3118364	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3118365	0.94[EUR][1000 genomes]
rs3118366	0.98[EUR][1000 genomes]
rs3118367	1.00[EUR][1000 genomes]
rs3129791	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3129794	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3129797	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3129798	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130837	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3130838	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130844	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130845	0.96[EUR][1000 genomes]
rs3130846	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs3130847	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130885	0.94[EUR][1000 genomes]
rs3130887	0.98[EUR][1000 genomes]
rs3130888	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130890	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3130891	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130892	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130893	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130894	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130895	0.94[EUR][1000 genomes]
rs3130896	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3131068	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3131069	0.96[EUR][1000 genomes]
rs3131071	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3131072	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3131073	0.93[EUR][1000 genomes]
rs3131075	0.96[EUR][1000 genomes]
rs3131076	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3131081	0.96[EUR][1000 genomes]
rs3131085	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3131093	0.98[EUR][1000 genomes]
rs3131094	1.00[EUR][1000 genomes]
rs3131095	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131096	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131097	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131101	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3131335	0.98[EUR][1000 genomes]
rs3131336	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131340	0.89[EUR][1000 genomes]
rs3131341	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131343	0.87[EUR][1000 genomes]
rs3131345	1.00[EUR][1000 genomes]
rs3132373	0.87[EUR][1000 genomes]
rs3132374	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3132376	1.00[EUR][1000 genomes]
rs3132378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132382	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3132384	1.00[EUR][1000 genomes]
rs3132385	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3132387	0.98[EUR][1000 genomes]
rs3132388	1.00[EUR][1000 genomes]
rs3132389	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3132391	1.00[EUR][1000 genomes]
rs3132392	1.00[EUR][1000 genomes]
rs3132393	0.98[EUR][1000 genomes]
rs3132394	0.98[EUR][1000 genomes]
rs3132395	0.98[EUR][1000 genomes]
rs3132396	0.89[EUR][1000 genomes]
rs3135293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135294	0.87[EUR][1000 genomes]
rs3135295	1.00[EUR][1000 genomes]
rs3135297	0.94[EUR][1000 genomes]
rs3135298	0.98[EUR][1000 genomes]
rs3135299	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3135300	1.00[EUR][1000 genomes]
rs3135302	1.00[EUR][1000 genomes]
rs3135304	1.00[EUR][1000 genomes]
rs3135306	1.00[EUR][1000 genomes]
rs3135307	1.00[EUR][1000 genomes]
rs3135309	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135310	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135311	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135312	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135313	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135316	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135317	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3135318	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3135325	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4324798	0.89[EUR][1000 genomes]
rs7760313	0.98[EUR][1000 genomes]
rs7761321	0.87[EUR][1000 genomes]
rs7764642	0.82[EUR][1000 genomes]
rs7766699	0.84[EUR][1000 genomes]
rs7767099	0.87[EUR][1000 genomes]
rs9257133	0.80[EUR][1000 genomes]
rs9257136	0.80[EUR][1000 genomes]
rs9257137	0.80[EUR][1000 genomes]
rs9257140	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9257167	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9257183	0.84[EUR][1000 genomes]
rs9257184	0.84[EUR][1000 genomes]
rs9257187	0.84[EUR][1000 genomes]
rs9257188	0.84[EUR][1000 genomes]
rs9257189	0.84[EUR][1000 genomes]
rs9257192	0.84[EUR][1000 genomes]
rs9257217	0.87[EUR][1000 genomes]
rs9257223	0.89[EUR][1000 genomes]
rs9257227	0.85[EUR][1000 genomes]
rs9257245	0.98[EUR][1000 genomes]
rs9257249	0.96[EUR][1000 genomes]
rs9257250	0.96[EUR][1000 genomes]
rs9257262	1.00[EUR][1000 genomes]
rs9257267	0.96[EUR][1000 genomes]
rs9257272	1.00[EUR][1000 genomes]
rs9257331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9257345	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3135308	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs3135308	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs3135308	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28849400-28852200	Weak transcription	Duodenum Mucosa	Duodenum
2	chr6:28849400-28863000	Weak transcription	Right Atrium	heart
3	chr6:28851000-28852800	Weak transcription	HepG2	liver
4	chr6:28851600-28852200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr6:28851600-28852200	Flanking Active TSS	Thymus	Thymus
6	chr6:28851800-28852200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr6:28851800-28852200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:28851800-28852200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
9	chr6:28851800-28852200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:28851800-28852400	Flanking Active TSS	Primary T cells from cord blood	blood
11	chr6:28851800-28852400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr6:28851800-28852800	Bivalent/Poised TSS	Primary B cells from cord blood	blood
13	chr6:28851800-28852800	Active TSS	GM12878-XiMat	blood
14	chr6:28851800-28853000	Flanking Active TSS	Dnd41	blood
15	chr6:28851800-28853400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
16	chr6:28852000-28852200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
17	chr6:28852000-28852200	Enhancers	Primary hematopoietic stem cells	blood
18	chr6:28852000-28852200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr6:28852000-28852400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr6:28852000-28852400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr6:28852000-28852400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr6:28852000-28852400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
23	chr6:28852000-28852400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr6:28852000-28852400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:28852000-28852400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
26	chr6:28852000-28852400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:28852000-28852400	Flanking Active TSS	Fetal Thymus	thymus
28	chr6:28852000-28852400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
29	chr6:28852000-28852600	ZNF genes & repeats	Fetal Intestine Small	intestine
30	chr6:28852000-28852600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
31	chr6:28852000-28853000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:28852000-28853200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
33	chr6:28852000-28853200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood

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