Variant report

Variant	rs3130845
Chromosome Location	chr6:28923367-28923368
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28804076..28806200-chr6:28922392..28924838,2	K562	blood:
2	chr6:28922600..28925578-chr6:28943937..28946823,4	K562	blood:
3	chr6:28921551..28923708-chr6:28958891..28962206,3	K562	blood:
4	chr6:28863289..28866205-chr6:28921133..28924025,2	K562	blood:
5	chr6:28848643..28851442-chr6:28923087..28926074,2	K562	blood:
6	chr6:28891742..28893312-chr6:28922794..28924812,2	K562	blood:
7	chr6:28920218..28924369-chr6:28968578..28972504,4	K562	blood:
8	chr6:28889277..28892149-chr6:28920165..28923545,3	K562	blood:
9	chr6:28918185..28920512-chr6:28921430..28924835,3	MCF-7	breast:
10	chr6:28916972..28925607-chr6:28947207..28951909,14	K562	blood:
11	chr6:28905933..28927444-chr6:28943937..28954526,53	K562	blood:
12	chr6:28676149..28677937-chr6:28921476..28924088,2	K562	blood:
13	chr6:28890510..28893121-chr6:28923251..28925362,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000224157	Chromatin interaction
ENSG00000263426	Chromatin interaction
ENSG00000227214	Chromatin interaction
ENSG00000204713	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1233620	0.80[EUR][1000 genomes]
rs1233623	0.80[EUR][1000 genomes]
rs13206458	1.00[EUR][1000 genomes]
rs3117146	0.92[EUR][1000 genomes]
rs3118357	0.96[EUR][1000 genomes]
rs3118359	0.96[EUR][1000 genomes]
rs3118360	0.89[EUR][1000 genomes]
rs3118361	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	0.85[EUR][1000 genomes]
rs3129794	0.92[EUR][1000 genomes]
rs3129797	0.92[EUR][1000 genomes]
rs3129798	0.92[EUR][1000 genomes]
rs3130837	0.96[EUR][1000 genomes]
rs3130838	0.96[EUR][1000 genomes]
rs3130844	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130846	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3130847	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	0.92[EUR][1000 genomes]
rs3130890	0.82[EUR][1000 genomes]
rs3130891	0.92[EUR][1000 genomes]
rs3130892	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130893	0.92[EUR][1000 genomes]
rs3130894	0.92[EUR][1000 genomes]
rs3130895	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3130896	0.92[EUR][1000 genomes]
rs3131068	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131069	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131071	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131072	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[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131081	0.92[EUR][1000 genomes]
rs3131085	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	0.96[EUR][1000 genomes]
rs3131340	0.85[EUR][1000 genomes]
rs3131341	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	0.96[EUR][1000 genomes]
rs3132382	1.00[EUR][1000 genomes]
rs3132384	0.96[EUR][1000 genomes]
rs3132385	0.96[EUR][1000 genomes]
rs3132387	0.94[EUR][1000 genomes]
rs3132388	0.96[EUR][1000 genomes]
rs3132389	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	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	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	0.96[EUR][1000 genomes]
rs3135317	0.92[EUR][1000 genomes]
rs3135318	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135325	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]
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	0.96[EUR][1000 genomes]
rs9257345	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
4	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
5	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
6	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
7	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
8	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
9	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3130845	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs3130845	BTN3A2	trans	lymphoblastoid	seeQTL
rs3130845	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs3130845	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28922000-28923400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr6:28922200-28923800	Enhancers	NHEK	skin
3	chr6:28922200-28928400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:28922200-28930600	Weak transcription	Right Atrium	heart
5	chr6:28922800-28923400	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr6:28922800-28923400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:28923000-28923400	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr6:28923000-28923400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr6:28923000-28923600	Flanking Active TSS	K562	blood
10	chr6:28923000-28928600	Weak transcription	HepG2	liver
11	chr6:28923200-28923400	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr6:28923200-28923400	Enhancers	Fetal Intestine Small	intestine

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