Variant report

Variant	rs3131071
Chromosome Location	chr6:28906922-28906923
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr6:28906922-28908259	Hela-S3	cervix:	n/a	n/a
2	CEBPB	chr6:28906903-28907138	A549	lung:	n/a	n/a
3	CEBPB	chr6:28906886-28907641	HepG2	liver:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28888957..28894217-chr6:28902105..28913114,27	MCF-7	breast:
2	chr6:28859278..28869415-chr6:28906395..28912460,18	K562	blood:
3	chr6:28863888..28865643-chr6:28906891..28908476,2	MCF-7	breast:
4	chr6:28694415..28696951-chr6:28906885..28909854,2	K562	blood:
5	chr6:28899297..28900909-chr6:28906173..28908577,2	MCF-7	breast:
6	chr6:28886838..28893375-chr6:28904762..28912890,19	K562	blood:
7	chr6:28846715..28849076-chr6:28906590..28908928,2	K562	blood:
8	chr6:28905933..28927444-chr6:28943937..28954526,53	K562	blood:

No data

Variant related genes	Relation type
C6orf100	TF binding region
ENSG00000227214	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000263426	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs1233599	0.80[EUR][1000 genomes]
rs1233600	0.80[EUR][1000 genomes]
rs1233604	0.80[EUR][1000 genomes]
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]
rs3131072	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]
rs9257140	1.00[AFR][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:4 , 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	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
rs3131071	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs3131071	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs3131071	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28903000-28907200	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr6:28903000-28907600	Weak transcription	Primary B cells from cord blood	blood
3	chr6:28903200-28907200	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr6:28903800-28907200	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr6:28904600-28907800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr6:28905200-28907800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr6:28905200-28907800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr6:28905200-28907800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr6:28905200-28907800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr6:28905400-28907800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr6:28905400-28907800	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr6:28905600-28907800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr6:28906600-28907200	Enhancers	K562	blood
14	chr6:28906600-28907400	Flanking Active TSS	HepG2	liver
15	chr6:28906600-28912600	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr6:28906800-28907200	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr6:28906800-28907200	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr6:28906800-28907800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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