Variant report

Variant	rs3898762
Chromosome Location	chr18:9575419-9575420
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr18:9575388-9575966	K562	blood:	n/a	chr18:9575785-9575796
2	RAD21	chr18:9575357-9575972	ECC-1	luminal epithelium:	n/a	n/a
3	CTCF	chr18:9575416-9576058	HCT-116	colon:	n/a	n/a
4	SMC3	chr18:9575344-9575984	SK-N-SH	brain:	n/a	n/a
5	RAD21	chr18:9575317-9576056	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr18:9575408-9575891	K562	blood:	n/a	n/a
7	EP300	chr18:9575280-9575811	K562	blood:	n/a	n/a
8	TBL1XR1	chr18:9575312-9575935	K562	blood:	n/a	n/a
9	NFIC	chr18:9575359-9576110	ECC-1	luminal epithelium:	n/a	n/a
10	RAD21	chr18:9575415-9575964	A549	lung:	n/a	n/a
11	RAD21	chr18:9575353-9576021	A549	lung:	n/a	n/a
12	CTCF	chr18:9575375-9575912	A549	lung:	n/a	n/a
13	CTCF	chr18:9575229-9576012	A549	lung:	n/a	n/a
14	RAD21	chr18:9575409-9575970	ECC-1	luminal epithelium:	n/a	n/a
15	RAD21	chr18:9575272-9576066	HCT-116	colon:	n/a	n/a
16	CTCF	chr18:9575300-9575450	NHEK	skin:	n/a	n/a
17	MAX	chr18:9575398-9575961	A549	lung:	n/a	n/a
18	CTCF	chr18:9575414-9575917	IMR90	lung:	n/a	n/a
19	ARID3A	chr18:9575364-9575899	K562	blood:	n/a	n/a
20	RAD21	chr18:9575321-9575976	HCT-116	colon:	n/a	n/a
21	CTCF	chr18:9575397-9575927	MCF-7	breast:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:9573929..9576042-chr18:9682222..9683938,2	K562	blood:
2	chr18:9575357..9576099-chr18:9683070..9683881,4	MCF-7	breast:
3	chr18:9575405..9579354-chr18:9587737..9592465,5	K562	blood:
4	chr18:9573898..9575587-chr18:9599993..9601990,2	K562	blood:
5	chr18:9566461..9572065-chr18:9572620..9578759,7	K562	blood:
6	chr18:9575156..9575854-chr18:9771216..9772160,6	K562	blood:
7	chr18:9575214..9576129-chr18:9951013..9951824,3	K562	blood:
8	chr18:9573383..9575778-chr18:9900229..9903029,2	K562	blood:
9	chr18:9574087..9575900-chr18:9670643..9673512,2	MCF-7	breast:
10	chr18:9575298..9576117-chr18:9611923..9612878,3	MCF-7	breast:
11	chr18:9561840..9564033-chr18:9575235..9576918,2	K562	blood:
12	chr18:9574062..9575945-chr18:9705155..9707070,2	MCF-7	breast:
13	chr18:9574087..9576896-chr18:9600490..9602058,2	K562	blood:
14	chr18:9571660..9575689-chr18:9612432..9614168,3	K562	blood:
15	chr18:9552433..9554256-chr18:9573786..9576485,2	K562	blood:
16	chr18:9566461..9572540-chr18:9573224..9580743,8	K562	blood:
17	chr18:9575217..9576135-chr18:9661275..9662526,6	MCF-7	breast:

No data

Variant related genes	Relation type
PPP4R1	TF binding region
ENSG00000154845	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10451359	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11081484	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11874827	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12458145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13381718	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28366801	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28838295	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28879133	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2903505	0.82[CEU][hapmap]
rs328994	0.86[JPT][hapmap]
rs3826562	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56817979	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57356844	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58359806	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60220573	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7231313	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7233002	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7239271	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7239728	0.87[CHB][hapmap]
rs745218	0.88[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes]
rs8085047	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9304040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9945701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9946235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9946612	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9948831	0.89[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes]
rs9949507	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9951382	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9961558	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9965762	0.88[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv833585	chr18:9401630-9597291	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	esv3693417	chr18:9512985-9693638	Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv458024	chr18:9558240-9828448	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv576448	chr18:9558240-9828448	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9544000-9575600	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr18:9545800-9583600	Strong transcription	Primary T cells fromperipheralblood	blood
3	chr18:9545800-9595200	Strong transcription	Dnd41	blood
4	chr18:9549600-9581800	Weak transcription	Psoas Muscle	Psoas
5	chr18:9551000-9612200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr18:9553200-9575800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr18:9553800-9582000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr18:9553800-9613600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr18:9554000-9576000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr18:9554400-9578400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr18:9555400-9580600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr18:9557800-9575800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr18:9558000-9580600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr18:9559000-9586800	Weak transcription	Small Intestine	intestine
15	chr18:9559600-9580600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr18:9559600-9587000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr18:9560200-9577600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr18:9560400-9577600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr18:9561000-9575800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr18:9563000-9581600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr18:9563200-9580600	Weak transcription	Aorta	Aorta
22	chr18:9563600-9577400	Weak transcription	Spleen	Spleen
23	chr18:9563600-9580600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr18:9563600-9591600	Weak transcription	Colonic Mucosa	Colon
25	chr18:9563600-9594800	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr18:9564200-9579600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr18:9565000-9576000	Weak transcription	Right Atrium	heart
28	chr18:9565000-9579400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr18:9565200-9575800	Strong transcription	Osteobl	bone
30	chr18:9565200-9594200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr18:9565600-9578000	Strong transcription	Placenta	Placenta
32	chr18:9566200-9575800	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr18:9566400-9577600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr18:9566600-9575800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr18:9566600-9577000	Strong transcription	HMEC	breast
36	chr18:9566800-9592600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr18:9566800-9594600	Strong transcription	HSMM	muscle
38	chr18:9567000-9576400	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr18:9567200-9577800	Strong transcription	NHEK	skin
40	chr18:9568600-9587600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr18:9569200-9578200	Weak transcription	Gastric	stomach
42	chr18:9569800-9576200	Strong transcription	Fetal Thymus	thymus
43	chr18:9569800-9582400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr18:9570400-9594400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr18:9570600-9575600	Weak transcription	Fetal Stomach	stomach
46	chr18:9570600-9577400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr18:9570600-9577400	Weak transcription	Lung	lung
48	chr18:9570600-9577400	Weak transcription	Pancreas	Pancrea
49	chr18:9570600-9580600	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr18:9570600-9580600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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