Variant report

Variant	rs10898440
Chromosome Location	chr11:85859916-85859917
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr11:85859017-85860130	K562	blood:	n/a	n/a
2	GATA1	chr11:85858844-85860019	K562	blood:	n/a	chr11:85859546-85859555
3	HMGN3	chr11:85859257-85859922	K562	blood:	n/a	n/a
4	RCOR1	chr11:85859187-85859955	K562	blood:	n/a	n/a
5	BHLHE40	chr11:85859382-85859941	K562	blood:	n/a	n/a
6	ARID3A	chr11:85859270-85860099	K562	blood:	n/a	n/a
7	TEAD4	chr11:85859282-85859935	K562	blood:	n/a	n/a
8	NR2F2	chr11:85859113-85860183	K562	blood:	n/a	n/a
9	NFYA	chr11:85859502-85860018	K562	blood:	n/a	n/a
10	IRF1	chr11:85859305-85860272	K562	blood:	n/a	n/a
11	IRF1	chr11:85859314-85860041	K562	blood:	n/a	n/a
12	TBL1XR1	chr11:85859365-85859933	K562	blood:	n/a	n/a
13	CCNT2	chr11:85859266-85859996	K562	blood:	n/a	n/a
14	GATA1	chr11:85859039-85859982	PBDE	blood:	n/a	chr11:85859546-85859555

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:85859878-85859928	AG10803	skin:	n/a
2	chr11:85859878-85859928	MCF-7	breast:	n/a
3	chr11:85859878-85859928	H1-hESC	embryonic stem cell:	embryo
4	chr11:85859878-85859928	AG09309	skin:	n/a
5	chr11:85859878-85859928	HCPEpiC	choroid plexus:	n/a
6	chr11:85859878-85859928	CMK	blood:	n/a
7	chr11:85859878-85859928	HEEpiC	esophagus:	n/a
8	chr11:85859878-85859928	NT2-D1	testis:	n/a
9	chr11:85859878-85859928	AG04450	lung:	fetal
10	chr11:85859878-85859928	HepG2	liver:	n/a
11	chr11:85859878-85859928	Hela-S3	cervix:	n/a
12	chr11:85859878-85859928	A549	lung:	n/a
13	chr11:85859878-85859928	T-47D	breast:	n/a
14	chr11:85859878-85859928	HNPCEpiC	eye:	n/a
15	chr11:85859878-85859928	BJ	skin:	n/a
16	chr11:85859878-85859928	HPAEpiC	pulmonary alveolar:	n/a
17	chr11:85859878-85859928	AG09319	gingival:	n/a
18	chr11:85859878-85859928	PrEC	prostate:	n/a
19	chr11:85859878-85859928	HRPEpiC	eye:	n/a
20	chr11:85859878-85859928	GM12878	blood:	n/a
21	chr11:85859878-85859928	IMR90	lung:	fetal
22	chr11:85859878-85859928	SK-N-MC	brain:	n/a
23	chr11:85859878-85859928	MCF10A-Er-Src	breast:	n/a
24	chr11:85859878-85859928	LNCaP	prostate:	n/a
25	chr11:85859878-85859928	GM12892	blood:	n/a
26	chr11:85859878-85859928	SK-N-SH	brain:	n/a
27	chr11:85859878-85859928	NH-A	brain:	n/a
28	chr11:85859878-85859928	NHDF-neo	bronchial:	n/a
29	chr11:85859878-85859928	HEK293	kidney:	embryo
30	chr11:85859878-85859928	HCM	heart:	n/a
31	chr11:85859878-85859928	HIPEpiC	eye:	n/a
32	chr11:85859878-85859928	RPTEC	kidney:	n/a
33	chr11:85859878-85859928	ECC-1	luminal epithelium:	n/a
34	chr11:85859878-85859928	HUVEC	blood vessel:	n/a
35	chr11:85859878-85859928	NHBE	bronchial:	n/a
36	chr11:85859878-85859928	Caco-2	colon:	n/a
37	chr11:85859878-85859928	AoSMC	blood vessel:	n/a
38	chr11:85859878-85859928	NB4	blood:	n/a
39	chr11:85859878-85859928	HAEpiC	amniotic membrane:	n/a
40	chr11:85859878-85859928	HL-60	blood:	n/a
41	chr11:85859878-85859928	SK-N-SH_RA	brain:	n/a
42	chr11:85859878-85859928	GM12891	blood:	n/a
43	chr11:85859878-85859928	ovcar-3	ovarian:	n/a
44	chr11:85859878-85859928	PANC-1	pancreas:	n/a
45	chr11:85859878-85859928	PFSK-1	brain:	n/a
46	chr11:85859878-85859928	ProgFib	skin:	n/a
47	chr11:85859878-85859928	HCT-116	colon:	n/a
48	chr11:85859878-85859928	HCF	heart:	n/a
49	chr11:85859878-85859928	Hepatocyte	liver:	n/a
50	chr11:85859878-85859928	SKMC	muscle:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr11:85778968..85782907-chr11:85858162..85860822,3	K562	blood:
2	chr11:85859696..85863993-chr11:85872249..85875647,5	K562	blood:
3	chr11:85859821..85862459-chr11:85922097..85923862,2	K562	blood:
4	chr11:85844772..85849892-chr11:85856973..85861809,6	K562	blood:
5	chr11:85858516..85861097-chr11:85882162..85885113,2	K562	blood:

No data

Variant related genes	Relation type
RNU6-560P	TF binding region
RNU6-560P	CpG island
ENSG00000073921	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10792830	0.87[ASN][1000 genomes]
rs10792831	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10792832	0.90[ASN][1000 genomes]
rs10898438	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10898439	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11234555	0.83[ASN][1000 genomes]
rs11234556	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2028338	0.87[ASN][1000 genomes]
rs2888903	0.87[ASN][1000 genomes]
rs3844143	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3851178	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3851179	0.90[ASN][1000 genomes]
rs3915642	0.86[ASN][1000 genomes]
rs472486	0.83[ASN][1000 genomes]
rs4944560	0.86[ASN][1000 genomes]
rs580887	0.83[ASN][1000 genomes]
rs7110631	0.92[ASN][1000 genomes]
rs7114331	0.88[ASN][1000 genomes]
rs7114401	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7129687	0.82[ASN][1000 genomes]
rs7941541	0.92[ASN][1000 genomes]
rs7952506	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9787874	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050948	chr11:85756325-85968665	Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv541117	chr11:85756325-85968665	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv832223	chr11:85845315-86015957	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85846400-85862200	Weak transcription	Psoas Muscle	Psoas
2	chr11:85848000-85861200	Weak transcription	Small Intestine	intestine
3	chr11:85848000-85861600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr11:85850400-85862600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr11:85852800-85862200	Weak transcription	Right Atrium	heart
6	chr11:85853200-85860200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr11:85853200-85860600	Weak transcription	Osteobl	bone
8	chr11:85854400-85862800	Weak transcription	Primary B cells from cord blood	blood
9	chr11:85854800-85862600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr11:85855000-85861800	Weak transcription	Adipose Nuclei	Adipose
11	chr11:85855000-85862000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr11:85855800-85862200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr11:85856000-85861800	Weak transcription	GM12878-XiMat	blood
14	chr11:85856200-85862200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr11:85856600-85861200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr11:85856600-85862000	Weak transcription	Fetal Kidney	kidney
17	chr11:85857000-85863600	Weak transcription	Stomach Mucosa	stomach
18	chr11:85857200-85861200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr11:85857200-85861200	Weak transcription	Fetal Intestine Large	intestine
20	chr11:85857200-85862200	Weak transcription	A549	lung
21	chr11:85857400-85861400	Weak transcription	Liver	Liver
22	chr11:85857400-85861800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr11:85857800-85860200	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr11:85858000-85862200	Enhancers	Brain Hippocampus Middle	brain
25	chr11:85858200-85860200	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr11:85858200-85860600	Enhancers	Ovary	ovary
27	chr11:85858200-85862400	Enhancers	Brain Cingulate Gyrus	brain
28	chr11:85858400-85861200	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr11:85858400-85861200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr11:85858400-85861200	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr11:85858400-85862000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr11:85858400-85862200	Weak transcription	Pancreas	Pancrea
33	chr11:85858400-85862400	Weak transcription	Primary B cells from peripheral blood	blood
34	chr11:85858600-85861200	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr11:85858600-85861800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr11:85858800-85860200	Enhancers	Brain Substantia Nigra	brain
37	chr11:85859000-85860000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr11:85859000-85860000	Flanking Active TSS	K562	blood
39	chr11:85859200-85860400	Enhancers	Brain Angular Gyrus	brain
40	chr11:85859200-85860600	Enhancers	Brain Anterior Caudate	brain
41	chr11:85859200-85861200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr11:85859200-85861200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr11:85859200-85861600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr11:85859400-85860000	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr11:85859400-85860000	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr11:85859400-85860200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr11:85859400-85860600	Enhancers	Fetal Lung	lung
48	chr11:85859400-85861200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr11:85859400-85861200	Weak transcription	HMEC	breast
50	chr11:85859600-85860000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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