Variant report

Variant	rs538473374
Chromosome Location	chr3:138051568-138051569
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	CTCF	chr3:138051365-138051619	Spleen_OC	spleen:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
2	CTCF	chr3:138051420-138051570	AG04449	skin:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
3	RAD21	chr3:138051257-138051761	HepG2	liver:	n/a	chr3:138051482-138051496 chr3:138051481-138051500
4	CTCF	chr3:138051392-138051580	HepG2	liver:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
5	CTCF	chr3:138051292-138051716	K562	blood:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
6	CTCF	chr3:138051356-138051618	Lung_OC	lung:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
7	CTCF	chr3:138051336-138051664	A549	lung:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
8	CTCF	chr3:138051420-138051570	HCPEpiC	choroid plexus:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
9	CTCF	chr3:138051440-138051590	HAc	cerebellar:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
10	CTCF	chr3:138051420-138051570	MCF-7	breast:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
11	CTCF	chr3:138051420-138051570	GM12871	blood:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
12	RAD21	chr3:138051325-138051696	HepG2	liver:	n/a	chr3:138051482-138051496 chr3:138051481-138051500
13	ZNF143	chr3:138051353-138051767	H1-hESC	embryonic stem cell:	n/a	n/a
14	RAD21	chr3:138051250-138051730	H1-hESC	embryonic stem cell:	n/a	chr3:138051482-138051496 chr3:138051481-138051500
15	CTCF	chr3:138051440-138051590	GM12866	blood:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
16	CTCF	chr3:138051305-138051658	ECC-1	luminal epithelium:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
17	CTCF	chr3:138051460-138051610	Caco-2	colon:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
18	CTCF	chr3:138051440-138051590	HEEpiC	esophagus:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
19	CTCF	chr3:138051420-138051570	GM12869	blood:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
20	CTCF	chr3:138051440-138051590	HA-sp	spinal cord:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
21	CTCF	chr3:138051440-138051590	SK-N-SH_RA	brain:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
22	CTCF	chr3:138051283-138051698	HCT-116	colon:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
23	RAD21	chr3:138051282-138051855	MCF-7	breast:	n/a	chr3:138051482-138051496 chr3:138051481-138051500
24	CTCF	chr3:138051420-138051570	HRPEpiC	eye:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
25	SMC3	chr3:138051318-138051688	HepG2	liver:	n/a	chr3:138051482-138051496
26	CTCF	chr3:138051420-138051570	HBMEC	blood vessel:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
27	RAD21	chr3:138051260-138051785	H1-hESC	embryonic stem cell:	n/a	chr3:138051482-138051496 chr3:138051481-138051500
28	CTCF	chr3:138051274-138051999	MCF-7	breast:	n/a	chr3:138051483-138051496 chr3:138051758-138051766 chr3:138051482-138051503 chr3:138051480-138051498
29	RAD21	chr3:138051340-138051688	GM12878	blood:	n/a	chr3:138051482-138051496 chr3:138051481-138051500
30	CTCF	chr3:138051379-138051647	GM12878	blood:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
31	CTCF	chr3:138051420-138051570	GM12868	blood:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
32	CTCF	chr3:138051420-138051570	HepG2	liver:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
33	CTCF	chr3:138051420-138051570	HCFaa	heart:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
34	CTCF	chr3:138051440-138051590	GM12873	blood:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
35	CTCF	chr3:138051293-138051701	T-47D	breast:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
36	RAD21	chr3:138051316-138051639	SK-N-SH_RA	brain:	n/a	chr3:138051482-138051496 chr3:138051481-138051500
37	CTCF	chr3:138051420-138051570	GM12864	blood:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
38	CTCF	chr3:138051332-138051625	T-47D	breast:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
39	CTCF	chr3:138051356-138051639	HUVEC	blood vessel:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
40	CTCF	chr3:138051420-138051570	GM12865	blood:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
41	CTCF	chr3:138051371-138051608	Kidney_OC	kidney:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
42	RAD21	chr3:138051370-138051704	A549	lung:	n/a	chr3:138051482-138051496 chr3:138051481-138051500
43	FOXA1	chr3:138051339-138051624	T-47D	breast:	n/a	chr3:138051367-138051379
44	CTCF	chr3:138051420-138051570	HPAF	blood vessel:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
45	RAD21	chr3:138051202-138051907	HCT-116	colon:	n/a	chr3:138051482-138051496 chr3:138051481-138051500
46	RAD21	chr3:138051316-138051710	HepG2	liver:	n/a	chr3:138051482-138051496 chr3:138051481-138051500
47	CTCF	chr3:138051420-138051570	SAEC	small airway:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
48	CTCF	chr3:138051540-138051690	HFF-Myc	foreskin:	n/a	n/a
49	CTCF	chr3:138051420-138051570	GM12873	blood:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498
50	CTCF	chr3:138051420-138051570	WERI-Rb-1	eye:	n/a	chr3:138051483-138051496 chr3:138051482-138051503 chr3:138051480-138051498

No.	Distal block	Cell Line	Cell type
1	chr3:138049031..138051913-chr3:138117150..138118923,2	MCF-7	breast:
2	chr3:138051022..138051610-chr3:138144950..138145530,2	MCF-7	breast:
3	chr3:138051070..138051808-chr3:138136099..138136657,2	MCF-7	breast:
4	chr3:138050301..138052204-chr3:138116487..138117341,9	MCF-7	breast:

Variant related genes	Relation type
NME9	TF binding region

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv528349	chr3:138025396-138132393	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1821595	chr3:138043128-138055402	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv1796956	chr3:138051423-138122781	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv1848610	chr3:138051423-138133412	Bivalent Enhancer Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138048600-138051600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:138048600-138057800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:138049000-138051600	Weak transcription	HMEC	breast
4	chr3:138049000-138053400	Weak transcription	Pancreas	Pancrea
5	chr3:138049000-138053600	Weak transcription	Ovary	ovary
6	chr3:138049000-138055000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:138049000-138056600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:138049200-138051600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:138049200-138051600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:138049200-138053600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr3:138049200-138054400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr3:138049200-138054400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr3:138049200-138054600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:138049200-138055000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:138049200-138055000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:138049200-138055200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:138049200-138055400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:138050200-138052000	Weak transcription	Gastric	stomach
19	chr3:138050600-138056200	Weak transcription	HSMM	muscle
20	chr3:138051400-138051600	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr3:138051400-138051600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:138051400-138051800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:138051400-138051800	Enhancers	Fetal Heart	heart

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