Variant report

Variant	rs10402405
Chromosome Location	chr19:36912925-36912926
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr19:36912266-36913072	H1-hESC	embryonic stem cell:	n/a	chr19:36912697-36912704 chr19:36912616-36912630 chr19:36912470-36912480 chr19:36912693-36912707
2	MAX	chr19:36912319-36912995	H1-hESC	embryonic stem cell:	n/a	n/a
3	E2F6	chr19:36912220-36913022	H1-hESC	embryonic stem cell:	n/a	chr19:36912697-36912704 chr19:36912616-36912630 chr19:36912470-36912480 chr19:36912693-36912707
4	MAX	chr19:36912292-36913041	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:36912880-36912930	HCM	heart:	n/a
2	chr19:36912880-36912930	GM06990	blood:	n/a
3	chr19:36912880-36912930	Caco-2	colon:	n/a
4	chr19:36912880-36912930	NB4	blood:	n/a
5	chr19:36912880-36912930	AG04450	lung:	fetal
6	chr19:36912880-36912930	ovcar-3	ovarian:	n/a
7	chr19:36912880-36912930	ProgFib	skin:	n/a
8	chr19:36912880-36912930	H1-hESC	embryonic stem cell:	embryo
9	chr19:36912880-36912930	HMEC	breast:	n/a
10	chr19:36912880-36912930	Hepatocyte	liver:	n/a
11	chr19:36912880-36912930	GM12892	blood:	n/a
12	chr19:36912880-36912930	IMR90	lung:	fetal
13	chr19:36912880-36912930	NHDF-neo	bronchial:	n/a
14	chr19:36912880-36912930	SKMC	muscle:	n/a
15	chr19:36912880-36912930	K562	blood:	n/a
16	chr19:36912880-36912930	AG09309	skin:	n/a
17	chr19:36912880-36912930	AG04449	skin:	fetal
18	chr19:36912880-36912930	NH-A	brain:	n/a
19	chr19:36912880-36912930	SK-N-SH	brain:	n/a
20	chr19:36912880-36912930	HAEpiC	amniotic membrane:	n/a
21	chr19:36912880-36912930	GM12878	blood:	n/a
22	chr19:36912880-36912930	SK-N-MC	brain:	n/a
23	chr19:36912880-36912930	HL-60	blood:	n/a
24	chr19:36912880-36912930	GM19239	blood:	n/a
25	chr19:36912880-36912930	HCPEpiC	choroid plexus:	n/a
26	chr19:36912880-36912930	NHBE	bronchial:	n/a
27	chr19:36912880-36912930	ECC-1	luminal epithelium:	n/a
28	chr19:36912880-36912930	PFSK-1	brain:	n/a
29	chr19:36912880-36912930	LNCaP	prostate:	n/a
30	chr19:36912880-36912930	HPAEpiC	pulmonary alveolar:	n/a
31	chr19:36912880-36912930	Jurkat	blood:	n/a
32	chr19:36912880-36912930	PrEC	prostate:	n/a
33	chr19:36912880-36912930	HNPCEpiC	eye:	n/a
34	chr19:36912880-36912930	CMK	blood:	n/a
35	chr19:36912880-36912930	RPTEC	kidney:	n/a
36	chr19:36912880-36912930	AoSMC	blood vessel:	n/a
37	chr19:36912880-36912930	HRCEpiC	kidney:	n/a
38	chr19:36912880-36912930	HCT-116	colon:	n/a
39	chr19:36912880-36912930	BJ	skin:	n/a
40	chr19:36912880-36912930	GM12891	blood:	n/a
41	chr19:36912880-36912930	PANC-1	pancreas:	n/a
42	chr19:36912880-36912930	SK-N-SH_RA	brain:	n/a
43	chr19:36912880-36912930	MCF10A-Er-Src	breast:	n/a
44	chr19:36912880-36912930	HRE	kidney:	n/a
45	chr19:36912880-36912930	HEEpiC	esophagus:	n/a
46	chr19:36912880-36912930	A549	lung:	n/a
47	chr19:36912880-36912930	BE2_C	brain:	n/a
48	chr19:36912880-36912930	HIPEpiC	eye:	n/a
49	chr19:36912880-36912930	T-47D	breast:	n/a
50	chr19:36912880-36912930	U87	brain:	n/a

No data

Variant related genes	Relation type
ZFP82	TF binding region
ZFP82	CpG island

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10404574	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10414054	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10418510	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10420610	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10426014	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10439091	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12459465	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12971694	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12976881	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2271844	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2385799	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2385800	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2385801	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2385803	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2385805	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2945945	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2945948	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2945949	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2945950	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2945951	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2945957	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2945961	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2945963	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2945971	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2945972	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2945992	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2945993	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2945995	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2967501	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2967504	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2967510	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2967512	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2967515	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2967517	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2967518	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2967521	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2967523	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2967524	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2967525	0.81[ASN][1000 genomes]
rs2967526	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2967543	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2972633	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs5021030	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58703752	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6417185	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6510541	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6510542	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7246106	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7251979	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7255260	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7255403	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8106095	0.81[AFR][1000 genomes]
rs8109320	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8109333	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8112312	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8182628	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833816	chr19:36824257-37034287	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1066026	chr19:36878441-36947928	ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv1067101	chr19:36901010-36956251	ZNF genes & repeats Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10402405	LINC00665	cis	Muscle Skeletal	GTEx
rs10402405	LOC284412	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36911400-36913200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr19:36911400-36913400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
3	chr19:36911800-36913400	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr19:36911800-36913600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
5	chr19:36912000-36913000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
6	chr19:36912000-36913000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
7	chr19:36912000-36913000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr19:36912000-36913000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
9	chr19:36912000-36913000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr19:36912000-36913000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
11	chr19:36912000-36913000	Active TSS	Brain Hippocampus Middle	brain
12	chr19:36912000-36913000	Bivalent/Poised TSS	Fetal Lung	lung
13	chr19:36912000-36913000	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
14	chr19:36912000-36913000	Flanking Active TSS	Placenta	Placenta
15	chr19:36912000-36913000	Active TSS	Placenta Amnion	Placenta Amnion
16	chr19:36912000-36913000	Active TSS	Rectal Smooth Muscle	rectum
17	chr19:36912000-36913000	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
18	chr19:36912000-36913000	ZNF genes & repeats	HSMM	muscle
19	chr19:36912000-36913200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
20	chr19:36912000-36913200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr19:36912000-36913200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr19:36912000-36913200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr19:36912000-36913200	Active TSS	Brain Anterior Caudate	brain
24	chr19:36912000-36913200	Active TSS	Brain Cingulate Gyrus	brain
25	chr19:36912000-36913200	Bivalent/Poised TSS	Fetal Brain Female	brain
26	chr19:36912000-36913200	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr19:36912000-36913200	ZNF genes & repeats	Gastric	stomach
28	chr19:36912000-36913200	ZNF genes & repeats	Lung	lung
29	chr19:36912000-36913200	ZNF genes & repeats	Spleen	Spleen
30	chr19:36912000-36913200	Active TSS	Osteobl	bone
31	chr19:36912000-36913400	Active TSS	Brain Angular Gyrus	brain
32	chr19:36912000-36913600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr19:36912200-36913000	Active TSS	H9 Cell Line	embryonic stem cell
34	chr19:36912200-36913000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr19:36912200-36913000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr19:36912200-36913000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
37	chr19:36912200-36913000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
38	chr19:36912200-36913000	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr19:36912200-36913000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
40	chr19:36912200-36913000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr19:36912200-36913000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr19:36912200-36913000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr19:36912200-36913000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr19:36912200-36913000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr19:36912200-36913000	ZNF genes & repeats	Colonic Mucosa	Colon
46	chr19:36912200-36913000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
47	chr19:36912200-36913000	Active TSS	Fetal Kidney	kidney
48	chr19:36912200-36913000	ZNF genes & repeats	Pancreas	Pancrea
49	chr19:36912200-36913000	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
50	chr19:36912200-36913000	Flanking Active TSS	HUVEC	blood vessel

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