Variant report

Variant	rs2765219
Chromosome Location	chr6:28770349-28770350
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28756573..28759569-chr6:28769791..28772080,4	K562	blood:
2	chr6:28769403..28772112-chr6:28910261..28912768,2	K562	blood:
3	chr6:28769803..28772263-chr6:28862688..28865946,3	MCF-7	breast:
4	chr6:28761012..28764011-chr6:28768099..28770643,2	K562	blood:
5	chr6:28768996..28771268-chr6:28774440..28778213,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM27-19	chr6:28770349-28770592	NONHSAT108485

Variant related genes	Relation type
ENSG00000204709	Chromatin interaction
ENSG00000265764	Chromatin interaction
ENSG00000224157	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs1002925	0.87[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	0.84[AFR][1000 genomes];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	1.00[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	0.87[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	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs209186	0.82[AFR][1000 genomes];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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2754764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2754767	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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	1.00[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	0.80[AFR][1000 genomes];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	0.90[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	0.92[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:6 , 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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2765219	NKAPL	cis	parietal	SCAN
rs2765219	ZKSCAN3	cis	cerebellum	SCAN
rs2765219	ZSCAN23	cis	parietal	SCAN
rs2765219	ZNF323	cis	cerebellum	SCAN
rs2765219	ZNF323	cis	parietal	SCAN
rs2765219	HIST1H2BH	cis	cerebellum	SCAN
rs2765219	ZSCAN23	cis	cerebellum	SCAN
rs2765219	ZSCAN16	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28763400-28770600	Weak transcription	HMEC	breast
2	chr6:28764600-28770400	Weak transcription	GM12878-XiMat	blood
3	chr6:28770200-28770400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:28770200-28770400	Flanking Active TSS	K562	blood
5	chr6:28770200-28771600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr6:28770200-28771800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
7	chr6:28770200-28771800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell

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