Variant report

Variant	rs57913184
Chromosome Location	chr3:46908706-46908707
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	RAD21	chr3:46908118-46908893	HCT-116	colon:	n/a	chr3:46908285-46908299 chr3:46908413-46908423 chr3:46908257-46908269 chr3:46908409-46908423 chr3:46908287-46908300 chr3:46908413-46908425 chr3:46908408-46908427
2	CTCF	chr3:46908087-46908783	K562	blood:	n/a	chr3:46908410-46908423 chr3:46908410-46908419 chr3:46908408-46908424 chr3:46908407-46908425 chr3:46908412-46908422 chr3:46908410-46908423 chr3:46908409-46908430
3	SMC3	chr3:46907854-46909100	SK-N-SH	brain:	n/a	chr3:46908409-46908423 chr3:46908413-46908423
4	CTCF	chr3:46908706-46908711	GM19240	blood:	n/a	n/a
5	RAD21	chr3:46908021-46908966	SK-N-SH	brain:	n/a	chr3:46908285-46908299 chr3:46908413-46908423 chr3:46908257-46908269 chr3:46908409-46908423 chr3:46908287-46908300 chr3:46908413-46908425 chr3:46908408-46908427
6	CTCF	chr3:46908680-46908830	BE2_C	brain:	n/a	n/a
7	CTCF	chr3:46907728-46908868	SK-N-SH	brain:	n/a	chr3:46908410-46908423 chr3:46908410-46908419 chr3:46908408-46908424 chr3:46908407-46908425 chr3:46908412-46908422 chr3:46908410-46908423 chr3:46908409-46908430
8	CTCF	chr3:46908664-46908721	GM12891	blood:	n/a	n/a
9	RAD21	chr3:46908158-46908769	ECC-1	luminal epithelium:	n/a	chr3:46908285-46908299 chr3:46908413-46908423 chr3:46908257-46908269 chr3:46908409-46908423 chr3:46908287-46908300 chr3:46908413-46908425 chr3:46908408-46908427
10	RAD21	chr3:46908137-46908708	H1-hESC	embryonic stem cell:	n/a	chr3:46908285-46908299 chr3:46908413-46908423 chr3:46908257-46908269 chr3:46908409-46908423 chr3:46908287-46908300 chr3:46908413-46908425 chr3:46908408-46908427
11	CTCF	chr3:46908680-46908830	HFF-Myc	foreskin:	n/a	n/a
12	RAD21	chr3:46908142-46908821	HCT-116	colon:	n/a	chr3:46908285-46908299 chr3:46908413-46908423 chr3:46908257-46908269 chr3:46908409-46908423 chr3:46908287-46908300 chr3:46908413-46908425 chr3:46908408-46908427
13	CTCF	chr3:46908109-46908799	HCT-116	colon:	n/a	chr3:46908410-46908423 chr3:46908410-46908419 chr3:46908408-46908424 chr3:46908407-46908425 chr3:46908412-46908422 chr3:46908410-46908423 chr3:46908409-46908430
14	CTCF	chr3:46907946-46908814	A549	lung:	n/a	chr3:46908410-46908423 chr3:46908410-46908419 chr3:46908408-46908424 chr3:46908407-46908425 chr3:46908412-46908422 chr3:46908410-46908423 chr3:46908409-46908430
15	CTCF	chr3:46907959-46908911	HCT-116	colon:	n/a	chr3:46908410-46908423 chr3:46908410-46908419 chr3:46908408-46908424 chr3:46908407-46908425 chr3:46908412-46908422 chr3:46908410-46908423 chr3:46908409-46908430
16	RAD21	chr3:46908161-46908721	A549	lung:	n/a	chr3:46908285-46908299 chr3:46908413-46908423 chr3:46908257-46908269 chr3:46908409-46908423 chr3:46908287-46908300 chr3:46908413-46908425 chr3:46908408-46908427

No.	Distal block	Cell Line	Cell type
1	chr3:46907919..46909420-chr3:46936321..46937362,8	MCF-7	breast:
2	chr3:46908423..46910395-chr3:46920080..46921760,2	K562	blood:
3	chr3:46888374..46889993-chr3:46908092..46909889,2	K562	blood:
4	chr3:46888493..46890387-chr3:46908192..46909889,2	K562	blood:
5	chr3:46704655..46705427-chr3:46908187..46908829,2	MCF-7	breast:
6	chr3:46907889..46909004-chr3:46936396..46937326,9	K562	blood:
7	chr3:46907930..46908808-chr3:46950756..46951658,3	K562	blood:
8	chr3:46907898..46909023-chr3:46936371..46937303,3	MCF-7	breast:
9	chr3:46908003..46908876-chr3:47412441..47413277,3	K562	blood:
10	chr3:46907320..46909923-chr3:46919093..46921760,2	K562	blood:
11	chr3:46908049..46912169-chr3:46912978..46916098,5	K562	blood:
12	chr3:46904622..46907361-chr3:46908422..46910821,2	K562	blood:
13	chr3:46906899..46908825-chr3:46935706..46937551,2	K562	blood:

Variant related genes	Relation type
MYL3	TF binding region
ENSG00000160801	Chromatin interaction
ENSG00000160808	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2233264	0.98[ASN][1000 genomes]
rs73833644	0.87[ASN][1000 genomes]
rs73833645	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	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv590205	chr3:46852679-46929546	Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1003979	chr3:46853374-46943854	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv590206	chr3:46873957-46935527	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv876752	chr3:46879831-46967040	Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv876753	chr3:46884552-46957298	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv876754	chr3:46884552-46967040	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
14	nsv590207	chr3:46903361-46919379	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46888000-46908800	Weak transcription	Esophagus	oesophagus
2	chr3:46901000-46909000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:46904600-46911600	Enhancers	Placenta	Placenta
4	chr3:46905200-46911400	Enhancers	Fetal Lung	lung
5	chr3:46905400-46910200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:46905600-46910400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:46905800-46909800	Enhancers	Fetal Stomach	stomach
8	chr3:46906000-46910000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr3:46906000-46911600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
10	chr3:46906200-46910400	Enhancers	Fetal Heart	heart
11	chr3:46906400-46908800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:46906600-46908800	Weak transcription	NHDF-Ad	bronchial
13	chr3:46906600-46910600	Enhancers	Right Ventricle	heart
14	chr3:46906800-46920000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:46907000-46909400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:46907200-46909000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr3:46907200-46909200	Weak transcription	HSMM	muscle
18	chr3:46907400-46908800	Weak transcription	Spleen	Spleen
19	chr3:46907800-46910200	Enhancers	Left Ventricle	heart
20	chr3:46907800-46910200	Enhancers	Right Atrium	heart
21	chr3:46907800-46910800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:46908200-46909800	Enhancers	Pancreas	Pancrea
23	chr3:46908200-46910000	Enhancers	Brain Cingulate Gyrus	brain
24	chr3:46908200-46910000	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr3:46908200-46910400	Enhancers	Fetal Muscle Leg	muscle
26	chr3:46908200-46910600	Enhancers	HSMMtube	muscle
27	chr3:46908400-46908800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:46908400-46908800	Enhancers	Rectal Smooth Muscle	rectum
29	chr3:46908400-46909000	Enhancers	Osteobl	bone
30	chr3:46908400-46909200	Enhancers	Brain Germinal Matrix	brain
31	chr3:46908400-46909200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr3:46908400-46909800	Enhancers	Fetal Intestine Large	intestine
33	chr3:46908400-46909800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr3:46908400-46910000	Enhancers	Brain Angular Gyrus	brain
35	chr3:46908400-46910000	Enhancers	Brain Substantia Nigra	brain
36	chr3:46908400-46910400	Enhancers	Colon Smooth Muscle	Colon
37	chr3:46908400-46911000	Enhancers	Brain Hippocampus Middle	brain
38	chr3:46908400-46911200	Enhancers	Ovary	ovary
39	chr3:46908400-46913200	Enhancers	Liver	Liver
40	chr3:46908600-46909000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:46908600-46909000	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr3:46908600-46909200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:46908600-46909400	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr3:46908600-46909600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr3:46908600-46909600	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr3:46908600-46909800	Enhancers	Brain Anterior Caudate	brain
47	chr3:46908600-46909800	Enhancers	Stomach Mucosa	stomach
48	chr3:46908600-46910000	Enhancers	Lung	lung
49	chr3:46908600-46910000	Enhancers	Psoas Muscle	Psoas
50	chr3:46908600-46910200	Enhancers	Colonic Mucosa	Colon

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