Variant report

Variant	rs2754767
Chromosome Location	chr6:28775241-28775242
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:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28774872..28779186-chr6:28780865..28786550,9	K562	blood:
2	chr6:28760359..28762539-chr6:28774291..28776179,2	K562	blood:
3	chr6:28768996..28771268-chr6:28774440..28778213,3	K562	blood:
4	chr6:28775179..28778043-chr6:28889400..28891921,3	MCF-7	breast:
5	chr6:28760359..28764219-chr6:28771578..28776179,5	K562	blood:
6	chr6:28774860..28778003-chr6:28805367..28807894,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM27-18	chr6:28773744-28776603	NONHSAT108486

No data

Variant related genes	Relation type
ENSG00000225173	Chromatin interaction
ENSG00000265764	Chromatin interaction
ENSG00000204713	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1002925	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233596	0.82[EUR][1000 genomes]
rs1233601	0.83[EUR][1000 genomes]
rs1233602	0.90[EUR][1000 genomes]
rs1233607	0.82[EUR][1000 genomes]
rs1233615	0.83[EUR][1000 genomes]
rs1233616	0.83[EUR][1000 genomes]
rs1233617	0.82[EUR][1000 genomes]
rs1235176	0.82[EUR][1000 genomes]
rs1237485	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1476016	0.86[EUR][1000 genomes]
rs169683	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1794587	0.90[EUR][1000 genomes]
rs184093	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2032500	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2071790	0.86[EUR][1000 genomes]
rs209122	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs209126	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs209128	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs209129	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs209137	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs209138	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs209148	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs209149	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs209152	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs209153	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs209160	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs209161	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs209163	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs209164	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs209169	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs209171	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs209173	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs209175	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs209176	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs209179	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs209182	0.87[EUR][1000 genomes]
rs209184	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs209186	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2157312	0.84[EUR][1000 genomes]
rs2157313	0.86[EUR][1000 genomes]
rs2208536	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2754764	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765218	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765219	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765229	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3129792	0.82[EUR][1000 genomes]
rs3130841	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3130842	0.86[EUR][1000 genomes]
rs3130886	0.84[EUR][1000 genomes]
rs3130889	0.86[EUR][1000 genomes]
rs3130897	0.86[EUR][1000 genomes]
rs3131070	0.86[EUR][1000 genomes]
rs3131074	0.86[EUR][1000 genomes]
rs3131077	0.85[EUR][1000 genomes]
rs3131102	0.89[EUR][1000 genomes]
rs3131342	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132371	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3132386	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3135303	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3135315	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3135321	0.82[EUR][1000 genomes]
rs3135322	0.84[EUR][1000 genomes]
rs3135323	0.85[EUR][1000 genomes]
rs3135324	0.85[EUR][1000 genomes]
rs3135327	0.82[EUR][1000 genomes]
rs3135328	0.86[EUR][1000 genomes]
rs377392	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs381808	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs386628	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs393431	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs526983	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6456857	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs763009	0.83[EUR][1000 genomes]
rs9257134	0.81[EUR][1000 genomes]
rs9257135	0.81[EUR][1000 genomes]
rs9257229	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534089	chr6:28636972-28841640	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv883517	chr6:28751727-28802149	Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv3384463	chr6:28759027-28776259	Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv2621756	chr6:28762692-28779791	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv2322180	chr6:28764675-28780578	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv9558	chr6:28770281-28785058	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3410540	chr6:28770455-28785112	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv3322630	chr6:28770519-28785092	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	esv3486939	chr6:28770525-28785051	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	esv3486940	chr6:28770525-28785051	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	esv3403106	chr6:28770790-28785189	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2754767	NKAPL	cis	parietal	SCAN
rs2754767	ZKSCAN3	cis	cerebellum	SCAN
rs2754767	ZSCAN23	cis	parietal	SCAN
rs2754767	ZSCAN23	cis	cerebellum	SCAN
rs2754767	ZNF323	cis	cerebellum	SCAN
rs2754767	HIST1H2BH	cis	cerebellum	SCAN
rs2754767	ZSCAN16	cis	parietal	SCAN
rs2754767	ZNF323	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28771400-28775800	Weak transcription	GM12878-XiMat	blood
2	chr6:28771800-28775600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:28772200-28775600	Weak transcription	Hela-S3	cervix
4	chr6:28772400-28775600	Weak transcription	K562	blood
5	chr6:28772800-28775800	Weak transcription	A549	lung
6	chr6:28774600-28775600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:28775200-28778200	Weak transcription	Right Atrium	heart

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