Variant report

Variant	rs377392
Chromosome Location	chr6:28784741-28784742
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28687325..28688855-chr6:28783516..28785419,2	K562	blood:
2	chr6:28187117..28189206-chr6:28783315..28785702,2	K562	blood:
3	chr6:28774872..28779186-chr6:28780865..28786550,9	K562	blood:
4	chr6:28722382..28724843-chr6:28784005..28786428,2	K562	blood:
5	chr6:28783316..28785641-chr6:28791797..28793442,2	K562	blood:
6	chr6:28688964..28691307-chr6:28783200..28785150,2	K562	blood:
7	chr6:28722382..28725655-chr6:28783034..28786428,3	K562	blood:

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

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

rs_ID	r²[population]
rs1002925	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1233596	0.81[EUR][1000 genomes]
rs1233601	0.82[EUR][1000 genomes]
rs1233602	0.89[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	0.81[EUR][1000 genomes]
rs1237485	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1476016	0.87[EUR][1000 genomes]
rs169683	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1794587	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs184093	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2032500	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2071790	0.86[EUR][1000 genomes]
rs209122	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs209126	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs209128	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs209129	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs209137	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs209138	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs209148	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs209149	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs209152	0.91[EUR][1000 genomes]
rs209153	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs209160	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs209161	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs209163	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs209164	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs209169	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs209171	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs209173	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs209175	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs209176	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs209179	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs209182	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs209184	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs209186	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2157312	0.84[EUR][1000 genomes]
rs2157313	0.86[EUR][1000 genomes]
rs2208536	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2754764	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2754767	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2765218	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2765219	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2765229	0.87[EUR][1000 genomes]
rs3129792	0.83[EUR][1000 genomes]
rs3129793	0.81[EUR][1000 genomes]
rs3130841	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3130842	0.87[EUR][1000 genomes]
rs3130886	0.84[EUR][1000 genomes]
rs3130889	0.87[EUR][1000 genomes]
rs3130897	0.87[EUR][1000 genomes]
rs3131070	0.87[EUR][1000 genomes]
rs3131074	0.87[EUR][1000 genomes]
rs3131077	0.86[EUR][1000 genomes]
rs3131102	0.90[EUR][1000 genomes]
rs3131342	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3132371	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3132386	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3135303	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3135315	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3135321	0.83[EUR][1000 genomes]
rs3135322	0.85[EUR][1000 genomes]
rs3135323	0.86[EUR][1000 genomes]
rs3135324	0.86[EUR][1000 genomes]
rs3135326	0.80[EUR][1000 genomes]
rs3135327	0.83[EUR][1000 genomes]
rs3135328	0.86[EUR][1000 genomes]
rs381808	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs386628	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs393431	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs526983	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6456857	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs763009	0.84[EUR][1000 genomes]
rs9257134	0.81[EUR][1000 genomes]
rs9257135	0.81[EUR][1000 genomes]
rs9257229	0.87[EUR][1000 genomes];0.82[ASN][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	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	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
4	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
5	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
6	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
7	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
8	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
9	nsv970724	chr6:28778144-28784760	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs377392	NKAPL	cis	parietal	SCAN
rs377392	ZSCAN23	cis	parietal	SCAN
rs377392	ZNF323	cis	parietal	SCAN
rs377392	ZKSCAN3	cis	cerebellum	SCAN
rs377392	ZNF323	cis	cerebellum	SCAN
rs377392	HIST1H2BH	cis	cerebellum	SCAN
rs377392	ZSCAN23	cis	cerebellum	SCAN
rs377392	ZSCAN16	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28783600-28784800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr6:28784000-28785000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
3	chr6:28784200-28785400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
4	chr6:28784200-28786000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr6:28784200-28786200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr6:28784400-28784800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:28784400-28784800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:28784400-28784800	Bivalent Enhancer	HUVEC	blood vessel
9	chr6:28784400-28785000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:28784400-28785000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:28784400-28785000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
12	chr6:28784400-28785000	Flanking Bivalent TSS/Enh	HepG2	liver
13	chr6:28784400-28785000	Flanking Active TSS	NHEK	skin
14	chr6:28784400-28785200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:28784400-28785200	Bivalent/Poised TSS	Fetal Brain Female	brain
16	chr6:28784400-28785400	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
17	chr6:28784400-28785600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:28784400-28785800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
19	chr6:28784400-28785800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:28784400-28786000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
21	chr6:28784400-28786000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:28784400-28786000	Active TSS	A549	lung
23	chr6:28784600-28784800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
24	chr6:28784600-28784800	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr6:28784600-28784800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:28784600-28784800	Bivalent Enhancer	Liver	Liver
27	chr6:28784600-28784800	Bivalent Enhancer	Placenta	Placenta
28	chr6:28784600-28784800	Active TSS	K562	blood
29	chr6:28784600-28784800	Bivalent/Poised TSS	NHLF	lung
30	chr6:28784600-28785000	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:28784600-28785000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:28784600-28785000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:28784600-28785000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
34	chr6:28784600-28785000	Bivalent/Poised TSS	Cortex derived primary cultured neurospheres	brain
35	chr6:28784600-28785000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
36	chr6:28784600-28785000	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
37	chr6:28784600-28785000	Flanking Active TSS	Osteobl	bone
38	chr6:28784600-28785400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:28784600-28785400	Bivalent/Poised TSS	NH-A	brain
40	chr6:28784600-28785600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr6:28784600-28785600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:28784600-28785600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr6:28784600-28785600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:28784600-28785600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:28784600-28785600	Active TSS	Hela-S3	cervix
46	chr6:28784600-28785800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr6:28784600-28785800	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr6:28784600-28785800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr6:28784600-28785800	Active TSS	HMEC	breast
50	chr6:28784600-28786000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell

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