Variant report

Variant	rs9295740
Chromosome Location	chr6:27689502-27689503
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:27686786..27690624-chr6:27717358..27721129,5	K562	blood:
2	chr6:27100798..27103607-chr6:27688775..27690811,2	K562	blood:
3	chr6:27687897..27691780-chr6:27691811..27694513,3	MCF-7	breast:
4	chr6:27665264..27666796-chr6:27688059..27690362,2	K562	blood:
5	chr6:27688928..27690631-chr6:27710497..27712546,2	MCF-7	breast:
6	chr6:27658926..27663446-chr6:27685398..27690588,6	K562	blood:
7	chr6:27659151..27662876-chr6:27687364..27691190,4	K562	blood:
8	chr6:27114795..27117088-chr6:27688794..27690487,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000184825	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000196787	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10214440	0.95[ASN][1000 genomes]
rs10484401	1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[ASN][1000 genomes]
rs1139226	0.91[ASN][1000 genomes]
rs12179134	0.80[EUR][1000 genomes]
rs13211701	0.81[ASN][1000 genomes]
rs13215072	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1985099	0.81[ASN][1000 genomes]
rs200468	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs200486	0.88[CEU][hapmap]
rs200956	0.89[LWK][hapmap];0.81[MEX][hapmap]
rs200969	0.89[LWK][hapmap]
rs201004	0.88[CEU][hapmap];0.81[MEX][hapmap]
rs2056923	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs2056925	0.94[ASN][1000 genomes]
rs2092075	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs2179094	0.82[ASN][1000 genomes]
rs2179095	0.87[CHB][hapmap];0.92[CHD][hapmap];0.81[ASN][1000 genomes]
rs2394000	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2893929	0.86[ASN][1000 genomes]
rs2893930	0.83[ASN][1000 genomes]
rs2893931	0.81[ASN][1000 genomes]
rs34752872	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35069907	0.84[ASN][1000 genomes]
rs35957409	0.90[ASN][1000 genomes]
rs4140646	0.83[ASN][1000 genomes]
rs4711163	0.83[ASN][1000 genomes]
rs4713118	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4713121	0.87[CHB][hapmap];0.84[ASN][1000 genomes]
rs573179	0.89[LWK][hapmap]
rs6901520	0.91[ASN][1000 genomes]
rs6902689	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6914924	0.91[ASN][1000 genomes]
rs6922574	0.95[ASN][1000 genomes]
rs6930992	0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6940116	0.85[EUR][1000 genomes]
rs742046	0.82[CHB][hapmap];0.92[CHD][hapmap];0.82[ASN][1000 genomes]
rs742047	1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[ASN][1000 genomes]
rs760587	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7756968	0.86[ASN][1000 genomes]
rs7759217	0.87[CHB][hapmap];0.92[CHD][hapmap];0.81[ASN][1000 genomes]
rs7760523	0.90[ASN][1000 genomes]
rs7772027	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7773070	0.87[CHB][hapmap];0.84[ASN][1000 genomes]
rs7776351	0.84[ASN][1000 genomes]
rs9283880	0.90[ASN][1000 genomes]
rs9283881	0.90[ASN][1000 genomes]
rs9283882	0.90[ASN][1000 genomes]
rs9283883	0.90[ASN][1000 genomes]
rs9295742	0.95[ASN][1000 genomes]
rs9295743	0.88[ASN][1000 genomes]
rs9295746	1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[ASN][1000 genomes]
rs9348774	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348775	0.95[ASN][1000 genomes]
rs9357045	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366700	0.95[ASN][1000 genomes]
rs9366702	0.81[ASN][1000 genomes]
rs9368528	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9368529	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9368530	0.82[ASN][1000 genomes]
rs9380010	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9380011	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9380012	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9393847	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9393848	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9461401	0.95[ASN][1000 genomes]
rs9461405	0.87[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs9461406	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs9468195	0.90[ASN][1000 genomes]
rs9468199	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9468200	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9468201	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9468203	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9468204	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9468206	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9468214	0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9468217	0.88[ASN][1000 genomes]
rs9468220	1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[ASN][1000 genomes]
rs9468223	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs9468229	0.81[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	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv883510	chr6:27550712-27730064	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
4	nsv1031337	chr6:27596676-27734884	Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv601204	chr6:27655564-27689502	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv601205	chr6:27656255-27730064	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	esv3327708	chr6:27683503-27692934	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9295740	BTN3A3	cis	parietal	SCAN
rs9295740	BTN3A2	trans	lymphoblastoid	seeQTL
rs9295740	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs9295740	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs9295740	HIST1H2AB	cis	parietal	SCAN
rs9295740	ZKSCAN3	cis	parietal	SCAN
rs9295740	HIST1H3A	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27681600-27692200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr6:27687800-27689800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:27688400-27689600	Flanking Active TSS	NHEK	skin
4	chr6:27688600-27689600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:27688600-27689600	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr6:27688600-27689600	Flanking Active TSS	GM12878-XiMat	blood
7	chr6:27688600-27689800	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr6:27688600-27689800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:27688600-27690000	Active TSS	H9 Cell Line	embryonic stem cell
10	chr6:27688600-27690000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:27688600-27690000	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr6:27688600-27690000	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr6:27688600-27690000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:27688600-27690200	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr6:27688800-27689600	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr6:27688800-27689600	Active TSS	A549	lung
17	chr6:27688800-27689800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:27688800-27690000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr6:27688800-27690000	Active TSS	H1 Cell Line	embryonic stem cell
20	chr6:27689000-27690000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr6:27689200-27689600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:27689200-27689800	Flanking Active TSS	K562	blood
23	chr6:27689400-27689600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:27689400-27689600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
25	chr6:27689400-27690200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell

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