Variant report

Variant	rs916569
Chromosome Location	chr6:30066097-30066098
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30039673..30045870-chr6:30065915..30071954,9	MCF-7	breast:
2	chr6:30059482..30063646-chr6:30064744..30071169,8	MCF-7	breast:
3	chr6:30036068..30037732-chr6:30063349..30066200,2	MCF-7	breast:
4	chr6:30031856..30036259-chr6:30064937..30071315,10	MCF-7	breast:
5	chr6:30027914..30030220-chr6:30065122..30067982,3	MCF-7	breast:
6	chr6:30063791..30066840-chr6:30067476..30070156,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066379	Chromatin interaction
ENSG00000204623	Chromatin interaction
ENSG00000204619	Chromatin interaction
ENSG00000204618	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10947051	0.81[ASN][1000 genomes]
rs10947052	0.81[ASN][1000 genomes]
rs1108052	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1108053	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1110446	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1110448	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1156533	0.91[ASN][1000 genomes]
rs11751554	0.86[ASN][1000 genomes]
rs11753939	0.80[ASN][1000 genomes]
rs11755853	0.81[ASN][1000 genomes]
rs11758516	0.81[ASN][1000 genomes]
rs11965379	0.80[ASN][1000 genomes]
rs11965540	0.80[ASN][1000 genomes]
rs11967911	0.98[ASN][1000 genomes]
rs11968367	0.86[ASN][1000 genomes]
rs11968434	0.86[ASN][1000 genomes]
rs1264694	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1264695	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264696	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264702	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12661731	0.91[ASN][1000 genomes]
rs12663534	0.81[ASN][1000 genomes]
rs17187791	0.98[ASN][1000 genomes]
rs17187805	0.98[ASN][1000 genomes]
rs17194146	0.89[ASN][1000 genomes]
rs17194153	0.98[ASN][1000 genomes]
rs17194160	0.98[ASN][1000 genomes]
rs17194174	0.98[ASN][1000 genomes]
rs2072110	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2240071	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2248289	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2285805	0.80[ASN][1000 genomes]
rs2394735	0.81[ASN][1000 genomes]
rs2523994	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2524005	1.00[CEU][hapmap]
rs2844796	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28454792	0.96[ASN][1000 genomes]
rs28771211	0.82[ASN][1000 genomes]
rs28780078	0.91[ASN][1000 genomes]
rs28780079	0.91[ASN][1000 genomes]
rs28780080	0.91[ASN][1000 genomes]
rs28780081	0.91[ASN][1000 genomes]
rs28780082	0.90[ASN][1000 genomes]
rs3188482	0.80[ASN][1000 genomes]
rs3807032	0.81[ASN][1000 genomes]
rs3807033	0.81[ASN][1000 genomes]
rs57195817	0.84[ASN][1000 genomes]
rs57518619	0.81[ASN][1000 genomes]
rs58099508	0.81[ASN][1000 genomes]
rs60418878	0.85[ASN][1000 genomes]
rs61666432	0.86[ASN][1000 genomes]
rs6457149	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73424274	0.85[ASN][1000 genomes]
rs73728107	0.80[ASN][1000 genomes]
rs7741418	0.91[ASN][1000 genomes]
rs7749793	0.98[ASN][1000 genomes]
rs7753935	0.98[ASN][1000 genomes]
rs7754005	0.98[ASN][1000 genomes]
rs7761563	0.91[ASN][1000 genomes]
rs7765810	0.91[ASN][1000 genomes]
rs7771071	0.86[ASN][1000 genomes]
rs916570	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261384	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432866	chr6:30026321-30080921	Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv884051	chr6:30059451-30071279	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv884050	chr6:30059451-30071330	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv884052	chr6:30059592-30067681	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv884053	chr6:30059592-30070538	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
6	nsv884054	chr6:30061361-30069525	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
7	nsv524794	chr6:30066031-30067892	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs916569	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs916569	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs916569	ZFP57	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30061000-30066800	Enhancers	Stomach Mucosa	stomach
2	chr6:30062000-30067000	Enhancers	Fetal Intestine Small	intestine
3	chr6:30062200-30067800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:30063400-30068400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:30063600-30068200	Weak transcription	HMEC	breast
6	chr6:30063800-30068000	Weak transcription	Lung	lung
7	chr6:30064000-30068000	Enhancers	HepG2	liver
8	chr6:30064400-30067000	Enhancers	Primary T cells from cord blood	blood
9	chr6:30064800-30066800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr6:30064800-30067200	Enhancers	K562	blood
11	chr6:30064800-30068400	Bivalent Enhancer	Fetal Intestine Large	intestine
12	chr6:30064800-30069600	Bivalent Enhancer	Fetal Thymus	thymus
13	chr6:30065000-30066600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
14	chr6:30065200-30066400	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr6:30065200-30066600	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr6:30065200-30066600	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr6:30065400-30066200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
18	chr6:30065400-30066200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
19	chr6:30065400-30066200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:30065400-30066200	Enhancers	NHEK	skin
21	chr6:30065400-30068800	Weak transcription	Gastric	stomach
22	chr6:30065600-30066200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
23	chr6:30065600-30066200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
24	chr6:30065600-30066400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:30065600-30066600	Bivalent Enhancer	Duodenum Mucosa	Duodenum
26	chr6:30065800-30066200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:30065800-30066400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
28	chr6:30065800-30066600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
29	chr6:30066000-30066200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:30066000-30066200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
31	chr6:30066000-30066200	Enhancers	Spleen	Spleen
32	chr6:30066000-30066400	Bivalent Enhancer	Colonic Mucosa	Colon
33	chr6:30066000-30066600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum

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