Variant report

Variant	rs17006705
Chromosome Location	chr3:20225823-20225824
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr3:20225431-20228757	MCF10A-Er-Src	breast:	n/a	chr3:20227701-20227712 chr3:20228378-20228392

No.	Distal block	Cell Line	Cell type
1	chr3:20053872..20056558-chr3:20225792..20227888,2	K562	blood:
2	chr3:19985145..19990136-chr3:20225418..20228312,6	K562	blood:
3	chr3:20225377..20229978-chr3:20232761..20235716,5	K562	blood:
4	chr3:20212661..20217850-chr3:20224065..20229766,9	K562	blood:
5	chr3:20215671..20219222-chr3:20225067..20228168,4	MCF-7	breast:
6	chr3:20211282..20213997-chr3:20225429..20228054,3	MCF-7	breast:
7	chr3:19987980..19990853-chr3:20225710..20227616,2	MCF-7	breast:

Variant related genes	Relation type
SGOL1	TF binding region
ENSG00000229468	Chromatin interaction
ENSG00000237485	Chromatin interaction
ENSG00000252442	Chromatin interaction
ENSG00000163576	Chromatin interaction
ENSG00000144566	Chromatin interaction
ENSG00000129810	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10510498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1581002	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17006645	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17006680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17006684	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17006703	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17006760	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17006762	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17497321	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2292226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2292227	1.00[CEU][hapmap]
rs2292229	0.92[ASN][1000 genomes]
rs3762631	0.93[AMR][1000 genomes]
rs3804573	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4273391	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60747537	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61280687	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6783444	1.00[CEU][hapmap]
rs6792672	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9310614	0.95[ASN][1000 genomes]
rs9878045	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv834627	chr3:20068115-20227975	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv433359	chr3:20090908-20587572	Enhancers Flanking Active TSS Active TSS Strong transcription Weak 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	19 gene(s)	inside rSNPs	diseases
7	nsv470450	chr3:20096735-20389045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv1001006	chr3:20110743-20752628	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536512	chr3:20110743-20752628	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	esv1829018	chr3:20116077-20596244	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers 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	19 gene(s)	inside rSNPs	diseases
11	esv1827700	chr3:20119716-20489086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
12	esv1830036	chr3:20121828-20278275	Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
13	esv1830599	chr3:20121828-20375643	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
14	esv1828816	chr3:20136508-20389045	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
15	esv1832674	chr3:20152772-20605302	Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
16	esv1831853	chr3:20157077-20615273	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
17	esv1833208	chr3:20157077-20638228	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
18	esv2422249	chr3:20163608-20626956	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
19	esv1826144	chr3:20164282-20638228	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
20	nsv1013532	chr3:20172889-20305612	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
21	nsv536513	chr3:20172889-20305612	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
22	esv1831289	chr3:20191506-20617984	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
23	esv1829973	chr3:20192578-20375260	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
24	esv1829847	chr3:20196923-20638228	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
25	nsv876597	chr3:20197364-20242143	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
26	esv1829457	chr3:20200232-20375260	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
27	esv1830113	chr3:20200232-20430932	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
28	esv3377463	chr3:20203472-20343029	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
29	esv3381923	chr3:20203492-20342999	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20167800-20226000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr3:20193800-20226600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:20195000-20226000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:20195400-20226000	Weak transcription	NHDF-Ad	bronchial
5	chr3:20195400-20226200	Weak transcription	NHLF	lung
6	chr3:20197000-20226200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr3:20197000-20226800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:20197400-20227000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:20197600-20226800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:20202600-20226400	Weak transcription	Fetal Intestine Large	intestine
11	chr3:20213200-20227000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:20215600-20226400	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr3:20216200-20226400	Weak transcription	HSMM	muscle
14	chr3:20216600-20226000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr3:20219400-20226800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:20220600-20226800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:20220800-20226800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr3:20220800-20226800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr3:20221000-20226000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:20221400-20226200	Weak transcription	Fetal Lung	lung
21	chr3:20221800-20226600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:20222000-20226000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr3:20222400-20226000	Weak transcription	NHEK	skin
24	chr3:20222600-20226000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:20222600-20226000	Weak transcription	NH-A	brain
26	chr3:20222600-20226600	Weak transcription	Fetal Muscle Leg	muscle
27	chr3:20222600-20227000	Weak transcription	Pancreas	Pancrea
28	chr3:20222800-20226800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr3:20222800-20227000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:20223000-20226800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr3:20223200-20226000	Weak transcription	Hela-S3	cervix
32	chr3:20223400-20226000	Weak transcription	HepG2	liver
33	chr3:20223400-20226800	Weak transcription	Fetal Intestine Small	intestine
34	chr3:20223400-20227000	Weak transcription	Left Ventricle	heart
35	chr3:20223600-20226400	Weak transcription	Fetal Stomach	stomach
36	chr3:20223800-20226200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr3:20223800-20226800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:20224000-20226000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:20224000-20226000	Weak transcription	Thymus	Thymus
40	chr3:20224200-20226000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr3:20224200-20226800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:20224600-20226800	Weak transcription	Gastric	stomach
43	chr3:20224600-20229000	Active TSS	GM12878-XiMat	blood
44	chr3:20224800-20226200	Weak transcription	Fetal Heart	heart
45	chr3:20225000-20226000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr3:20225000-20226000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:20225000-20226000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:20225000-20226200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:20225200-20226000	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr3:20225200-20226000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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