Variant report

Variant	rs12049769
Chromosome Location	chr10:43332491-43332492
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr10:43332165-43332512	MCF-7	breast:	n/a	n/a
2	CTCF	chr10:43332108-43332701	SK-N-SH	brain:	n/a	chr10:43332395-43332408 chr10:43332395-43332408 chr10:43332301-43332308
3	MXI1	chr10:43331906-43332972	SK-N-SH	brain:	n/a	n/a
4	HA-E2F1	chr10:43332216-43333087	MCF-7	breast:	n/a	chr10:43332393-43332402
5	RAD21	chr10:43331952-43332700	SK-N-SH	brain:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:43332443-43332493	ovcar-3	ovarian:	n/a
2	chr10:43332443-43332493	MCF-7	breast:	n/a
3	chr10:43332443-43332493	U87	brain:	n/a
4	chr10:43332443-43332493	HRCEpiC	kidney:	n/a
5	chr10:43332443-43332493	Hela-S3	cervix:	n/a
6	chr10:43332443-43332493	PrEC	prostate:	n/a
7	chr10:43332443-43332493	HRPEpiC	eye:	n/a
8	chr10:43332443-43332493	Caco-2	colon:	n/a
9	chr10:43332443-43332493	HCPEpiC	choroid plexus:	n/a
10	chr10:43332443-43332493	HEK293	kidney:	embryo
11	chr10:43332443-43332493	HL-60	blood:	n/a
12	chr10:43332443-43332493	SAEC	small airway:	n/a
13	chr10:43332443-43332493	SKMC	muscle:	n/a
14	chr10:43332443-43332493	NHDF-neo	bronchial:	n/a
15	chr10:43332443-43332493	HCT-116	colon:	n/a
16	chr10:43332443-43332493	Jurkat	blood:	n/a
17	chr10:43332443-43332493	PANC-1	pancreas:	n/a
18	chr10:43332443-43332493	HIPEpiC	eye:	n/a
19	chr10:43332443-43332493	H1-hESC	embryonic stem cell:	embryo
20	chr10:43332443-43332493	BE2_C	brain:	n/a
21	chr10:43332443-43332493	PFSK-1	brain:	n/a
22	chr10:43332443-43332493	AG04449	skin:	fetal
23	chr10:43332443-43332493	BJ	skin:	n/a
24	chr10:43332443-43332493	HEEpiC	esophagus:	n/a
25	chr10:43332443-43332493	SK-N-SH	brain:	n/a
26	chr10:43332443-43332493	GM19239	blood:	n/a
27	chr10:43332443-43332493	AG09319	gingival:	n/a
28	chr10:43332443-43332493	ECC-1	luminal epithelium:	n/a
29	chr10:43332443-43332493	HNPCEpiC	eye:	n/a
30	chr10:43332443-43332493	HPAEpiC	pulmonary alveolar:	n/a
31	chr10:43332443-43332493	GM12878	blood:	n/a
32	chr10:43332443-43332493	K562	blood:	n/a
33	chr10:43332443-43332493	MCF10A-Er-Src	breast:	n/a
34	chr10:43332443-43332493	NT2-D1	testis:	n/a
35	chr10:43332443-43332493	AG04450	lung:	fetal
36	chr10:43332443-43332493	HMEC	breast:	n/a
37	chr10:43332443-43332493	NH-A	brain:	n/a
38	chr10:43332443-43332493	SK-N-MC	brain:	n/a
39	chr10:43332443-43332493	HCF	heart:	n/a
40	chr10:43332443-43332493	GM12892	blood:	n/a
41	chr10:43332443-43332493	Hepatocyte	liver:	n/a
42	chr10:43332443-43332493	GM06990	blood:	n/a
43	chr10:43332443-43332493	LNCaP	prostate:	n/a
44	chr10:43332443-43332493	CMK	blood:	n/a
45	chr10:43332443-43332493	NB4	blood:	n/a
46	chr10:43332443-43332493	HAEpiC	amniotic membrane:	n/a
47	chr10:43332443-43332493	HepG2	liver:	n/a
48	chr10:43332443-43332493	GM12891	blood:	n/a
49	chr10:43332443-43332493	RPTEC	kidney:	n/a
50	chr10:43332443-43332493	SK-N-SH_RA	brain:	n/a

No data

Variant related genes	Relation type
RNU6-885P	TF binding region
RNU6-885P	CpG island

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10900269	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10900274	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10900275	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11239767	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11239769	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11239772	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11239779	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11239786	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11597306	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12049745	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12762093	0.84[AFR][1000 genomes]
rs12764004	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12768318	0.84[AFR][1000 genomes]
rs12769004	0.84[AFR][1000 genomes]
rs12771057	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12774683	0.84[AFR][1000 genomes]
rs12775553	0.84[AFR][1000 genomes]
rs3982199	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4119177	0.84[AFR][1000 genomes]
rs4949036	1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4949038	0.84[AFR][1000 genomes]
rs7393563	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550672	chr10:42753190-43441729	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv533331	chr10:42830221-43356410	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1042764	chr10:42846383-43511712	Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1050394	chr10:42890663-43604956	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats 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 miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv540573	chr10:42890663-43604956	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers 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 miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	esv2758216	chr10:42965131-43510191	Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	esv2759746	chr10:42965131-43510191	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	esv2757381	chr10:43104068-43352995	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv1047838	chr10:43234590-43379219	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
11	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
12	esv14695	chr10:43301539-43355457	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
13	nsv8627	chr10:43324929-43354934	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island miRNA target site	1 gene(s)	inside rSNPs	diseases
14	esv1842859	chr10:43327115-43334095	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43320000-43332600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr10:43321400-43332800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr10:43327200-43332600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr10:43327200-43332800	Weak transcription	Spleen	Spleen
5	chr10:43327600-43332800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr10:43328200-43332600	Weak transcription	Brain Substantia Nigra	brain
7	chr10:43328200-43332600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr10:43328200-43332600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr10:43328200-43333800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr10:43331600-43333000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr10:43331800-43333000	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr10:43332000-43332600	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr10:43332000-43332600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr10:43332000-43333000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr10:43332000-43333000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
16	chr10:43332200-43332600	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr10:43332200-43332600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr10:43332200-43332600	Enhancers	Primary B cells from peripheral blood	blood
19	chr10:43332200-43332600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr10:43332200-43332600	Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr10:43332200-43332600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr10:43332200-43332600	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr10:43332200-43332600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
24	chr10:43332200-43332600	Enhancers	Placenta	Placenta
25	chr10:43332200-43332600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
26	chr10:43332200-43332600	Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr10:43332200-43332600	Active TSS	NHLF	lung
28	chr10:43332200-43332800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
29	chr10:43332200-43332800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr10:43332200-43332800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr10:43332200-43332800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr10:43332200-43332800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr10:43332200-43332800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr10:43332200-43332800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr10:43332200-43332800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
36	chr10:43332200-43332800	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr10:43332200-43332800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr10:43332200-43332800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr10:43332200-43332800	Active TSS	Brain Anterior Caudate	brain
40	chr10:43332200-43332800	Active TSS	Brain Cingulate Gyrus	brain
41	chr10:43332200-43332800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
42	chr10:43332200-43332800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr10:43332200-43332800	Active TSS	Colon Smooth Muscle	Colon
44	chr10:43332200-43332800	Active TSS	Duodenum Mucosa	Duodenum
45	chr10:43332200-43332800	Bivalent Enhancer	Fetal Brain Male	brain
46	chr10:43332200-43332800	Enhancers	Lung	lung
47	chr10:43332200-43332800	Enhancers	Ovary	ovary
48	chr10:43332200-43332800	Bivalent/Poised TSS	Thymus	Thymus
49	chr10:43332200-43333000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
50	chr10:43332200-43333000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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