Variant report

Variant	rs62280630
Chromosome Location	chr3:137837838-137837839
allele	C/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	chr3:137837798-137838047	Lung_OC	lung:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
2	FOXP2	chr3:137837697-137838078	SK-N-MC	brain:	n/a	n/a
3	RAD21	chr3:137837750-137838081	GM12878	blood:	n/a	chr3:137837902-137837921 chr3:137837904-137837916
4	CREB1	chr3:137837723-137838045	A549	lung:	n/a	n/a
5	CTCF	chr3:137837820-137837970	HPF	lung:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
6	ARID3A	chr3:137837762-137838035	HepG2	liver:	n/a	n/a
7	CTCF	chr3:137837745-137838055	NHEK	skin:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
8	ZNF143	chr3:137837741-137838067	K562	blood:	n/a	chr3:137837972-137837981
9	UBTF	chr3:137837800-137837991	K562	blood:	n/a	n/a
10	CTCF	chr3:137837780-137838056	ProgFib	skin:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
11	MAFK	chr3:137837736-137837931	HepG2	liver:	n/a	n/a
12	CTCF	chr3:137837794-137838048	SK-N-SH_RA	brain:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
13	CTCF	chr3:137837820-137837970	HCT-116	colon:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
14	CTCF	chr3:137837723-137838046	HepG2	liver:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
15	CTCF	chr3:137837800-137838041	GM10248	blood:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
16	CTCF	chr3:137837701-137838032	ECC-1	luminal epithelium:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
17	CTCF	chr3:137837820-137837970	GM12864	blood:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
18	CTCF	chr3:137837800-137837950	GM12869	blood:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
19	CTCF	chr3:137837732-137838076	GM12892	blood:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
20	CTCF	chr3:137837800-137837950	HFF-Myc	foreskin:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
21	CTCF	chr3:137837674-137838043	GM12891	blood:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
22	CTCF	chr3:137837696-137838216	IMR90	lung:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
23	CTCF	chr3:137837742-137837989	T-47D	breast:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
24	RAD21	chr3:137837719-137838147	HepG2	liver:	n/a	chr3:137837902-137837921 chr3:137837904-137837916
25	CTCF	chr3:137837805-137837980	A549	lung:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
26	CTCF	chr3:137837780-137837930	GM06990	blood:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
27	RAD21	chr3:137837473-137838190	HCT-116	colon:	n/a	chr3:137837902-137837921 chr3:137837904-137837916
28	CTCF	chr3:137837780-137837930	HRPEpiC	eye:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
29	CTCF	chr3:137837807-137838017	GM20000	blood:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
30	RAD21	chr3:137837709-137838145	Hela-S3	cervix:	n/a	chr3:137837902-137837921 chr3:137837904-137837916
31	ZNF143	chr3:137837715-137838105	GM12878	blood:	n/a	chr3:137837972-137837981
32	RFX5	chr3:137837816-137838063	GM12878	blood:	n/a	n/a
33	CTCF	chr3:137837769-137838054	A549	lung:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
34	CTCF	chr3:137837804-137838028	Pancreas_OC	pancreas:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
35	CTCF	chr3:137837820-137837970	SAEC	small airway:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
36	CTCF	chr3:137837820-137837970	AG04449	skin:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
37	RAD21	chr3:137837665-137838125	IMR90	lung:	n/a	chr3:137837902-137837921 chr3:137837904-137837916
38	CTCF	chr3:137837820-137837970	Hela-S3	cervix:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
39	WRNIP1	chr3:137837754-137838011	GM12878	blood:	n/a	n/a
40	CHD2	chr3:137837780-137837943	HepG2	liver:	n/a	n/a
41	RAD21	chr3:137837549-137838078	SK-N-SH_RA	brain:	n/a	chr3:137837902-137837921 chr3:137837904-137837916
42	CTCF	chr3:137837644-137838041	H1-hESC	embryonic stem cell:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
43	ZNF143	chr3:137837730-137838097	H1-hESC	embryonic stem cell:	n/a	chr3:137837972-137837981
44	FOXM1	chr3:137837640-137838132	GM12878	blood:	n/a	n/a
45	CTCF	chr3:137837785-137838048	LNCaP	prostate:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
46	JUND	chr3:137837768-137837971	HepG2	liver:	n/a	n/a
47	CTCF	chr3:137837727-137838072	ECC-1	luminal epithelium:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
48	SPI1	chr3:137837785-137838102	HL-60	blood:	n/a	n/a
49	CTCF	chr3:137837665-137838109	T-47D	breast:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922
50	CTCF	chr3:137837820-137837970	HVMF	connective:	n/a	chr3:137837906-137837919 chr3:137837899-137837920 chr3:137837904-137837922

No.	Distal block	Cell Line	Cell type
1	chr3:137820273..137821044-chr3:137837392..137837964,2	MCF-7	breast:
2	chr3:137786807..137788879-chr3:137836537..137838505,22	MCF-7	breast:
3	chr3:137785795..137788680-chr3:137836157..137838933,3	MCF-7	breast:
4	chr3:137787211..137788408-chr3:137837411..137838466,26	MCF-7	breast:
5	chr3:137789176..137789822-chr3:137837460..137838165,2	MCF-7	breast:
6	chr3:137787348..137788077-chr3:137837494..137838376,4	K562	blood:

Variant related genes	Relation type
DZIP1L	TF binding region
ENSG00000158163	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs62280627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62280645	1.00[AFR][1000 genomes];0.85[EUR][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	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	esv2757890	chr3:137611789-137933835	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv2759180	chr3:137611789-137933835	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription 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	16 gene(s)	inside rSNPs	diseases
4	esv2751978	chr3:137715302-137890750	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1007857	chr3:137767454-137843106	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS 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:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:137834800-137843000	Weak transcription	Placenta	Placenta
2	chr3:137834800-137843600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:137835000-137843600	Weak transcription	Right Ventricle	heart
4	chr3:137835200-137843200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr3:137835200-137843600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:137835200-137843600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:137835200-137843600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:137835400-137843400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:137835400-137844200	Weak transcription	A549	lung
10	chr3:137835800-137843600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:137836800-137838000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:137836800-137838000	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr3:137836800-137838000	Enhancers	Adipose Nuclei	Adipose
14	chr3:137837000-137838000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:137837200-137838200	Enhancers	Fetal Heart	heart
16	chr3:137837400-137838000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:137837400-137838000	Enhancers	NHDF-Ad	bronchial
18	chr3:137837400-137838000	Enhancers	NHLF	lung
19	chr3:137837400-137838000	Enhancers	Osteobl	bone
20	chr3:137837400-137838400	Enhancers	Fetal Muscle Leg	muscle
21	chr3:137837400-137838600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:137837600-137838000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:137837600-137838200	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr3:137837600-137838400	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr3:137837600-137838400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:137837600-137838400	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr3:137837600-137838400	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr3:137837600-137838400	Enhancers	Fetal Muscle Trunk	muscle
29	chr3:137837600-137838400	Enhancers	Fetal Stomach	stomach
30	chr3:137837600-137838400	Enhancers	Stomach Mucosa	stomach
31	chr3:137837600-137838400	Enhancers	Hela-S3	cervix
32	chr3:137837600-137838400	Enhancers	HSMM	muscle
33	chr3:137837600-137839600	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr3:137837800-137838200	Enhancers	HepG2	liver
35	chr3:137837800-137838400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:137837800-137838400	Enhancers	Spleen	Spleen

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