Variant report

Variant	rs62072540
Chromosome Location	chr17:18225228-18225229
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:18225222-18225277	MCF10A-Er-Src	breast:	n/a	n/a
2	CTCF	chr17:18225100-18225250	AG09319	gingival:	n/a	n/a
3	POLR2A	chr17:18224606-18225600	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:18224131..18225984-chr17:18227061..18229677,2	K562	blood:
2	chr17:18224827..18226997-chr17:18265358..18268214,2	MCF-7	breast:
3	chr17:18223830..18226136-chr17:18229956..18231632,3	MCF-7	breast:
4	chr17:18217609..18225680-chr17:18226125..18232187,14	K562	blood:
5	chr17:18163811..18165499-chr17:18223440..18225988,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000267350	TF binding region
ENSG00000267350	Chromatin interaction
ENSG00000177427	Chromatin interaction
ENSG00000176974	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs11078415	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11867855	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11867895	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11868708	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11869515	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11869952	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11871761	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11872031	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12449313	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12450760	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12451555	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12451698	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12451807	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12939851	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16961114	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16961133	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16961153	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1925	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1962949	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1962950	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071242	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2273029	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2290502	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2290503	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2290504	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2290505	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2294913	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28364628	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35738574	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3817992	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3829956	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3862147	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3889544	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4386179	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4450455	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4500798	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4556848	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4925151	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4925177	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4925178	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57490980	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57697650	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59366579	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62072507	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62072509	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62072511	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62072515	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62072537	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62072541	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072544	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62072545	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62072546	0.80[EUR][1000 genomes]
rs6502641	0.85[EUR][1000 genomes]
rs7211573	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7215678	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7405677	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7498	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8081042	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8081155	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8081343	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9901707	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9909104	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9910090	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9913139	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][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	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
5	nsv833386	chr17:18170261-18332726	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv1057081	chr17:18171516-18256347	Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv543247	chr17:18171516-18256347	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1062368	chr17:18180747-18259234	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv833387	chr17:18200081-18378155	Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	esv1806346	chr17:18200081-18446384	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
11	esv1812661	chr17:18200081-18446384	Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
12	nsv428333	chr17:18200081-18446384	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
13	nsv427992	chr17:18200081-19192047	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
14	nsv521075	chr17:18220770-18227081	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 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	chr17:18219400-18227200	Genic enhancers	Primary T cells fromperipheralblood	blood
2	chr17:18219400-18266000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr17:18219600-18226000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr17:18219800-18226000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr17:18220000-18226000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr17:18220200-18228000	Weak transcription	Fetal Kidney	kidney
7	chr17:18220400-18228000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr17:18221400-18226000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr17:18221600-18225800	Weak transcription	Aorta	Aorta
10	chr17:18221600-18225800	Weak transcription	HSMMtube	muscle
11	chr17:18221600-18226200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr17:18221600-18226200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr17:18221800-18225800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr17:18221800-18226000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr17:18222200-18225800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr17:18222200-18226000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr17:18222400-18225600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr17:18222400-18227200	Weak transcription	HUVEC	blood vessel
19	chr17:18222400-18266200	Weak transcription	Small Intestine	intestine
20	chr17:18222600-18226000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr17:18222600-18227200	Weak transcription	Psoas Muscle	Psoas
22	chr17:18222600-18240800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr17:18222600-18243200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr17:18222800-18226200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr17:18222800-18236800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr17:18223000-18225600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr17:18223000-18225800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr17:18223000-18226000	Weak transcription	Brain Substantia Nigra	brain
29	chr17:18223000-18226200	Weak transcription	Hela-S3	cervix
30	chr17:18223000-18228200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr17:18223400-18228400	Strong transcription	Primary B cells from cord blood	blood
32	chr17:18223400-18235400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr17:18223600-18226000	Weak transcription	Fetal Lung	lung
34	chr17:18223600-18240800	Strong transcription	Fetal Muscle Leg	muscle
35	chr17:18223600-18265400	Strong transcription	Fetal Stomach	stomach
36	chr17:18223800-18225800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr17:18223800-18225800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr17:18223800-18226000	Weak transcription	Stomach Mucosa	stomach
39	chr17:18223800-18226200	Weak transcription	Osteobl	bone
40	chr17:18223800-18226800	Weak transcription	NHDF-Ad	bronchial
41	chr17:18223800-18227400	Weak transcription	NH-A	brain
42	chr17:18223800-18229200	Strong transcription	NHEK	skin
43	chr17:18223800-18236800	Strong transcription	Primary T cells from cord blood	blood
44	chr17:18223800-18236800	Strong transcription	Lung	lung
45	chr17:18223800-18240800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr17:18223800-18253600	Strong transcription	Thymus	Thymus
47	chr17:18224000-18226000	Weak transcription	HMEC	breast
48	chr17:18224000-18231000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
49	chr17:18224000-18236600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr17:18224000-18236600	Strong transcription	Fetal Intestine Large	intestine

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