Variant report

Variant	rs377731401
Chromosome Location	chr3:52833365-52833366
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	chr3:52833105-52833400	HepG2	liver:	n/a	chr3:52833254-52833273
2	CTCF	chr3:52833033-52833387	H1-hESC	embryonic stem cell:	n/a	chr3:52833256-52833274
3	CTCF	chr3:52833220-52833370	GM12871	blood:	n/a	chr3:52833256-52833274
4	RAD21	chr3:52833001-52833471	H1-hESC	embryonic stem cell:	n/a	chr3:52833254-52833273
5	CTCF	chr3:52833149-52833381	Gliobla	brain:	n/a	chr3:52833256-52833274
6	GABPA	chr3:52833050-52833386	H1-hESC	embryonic stem cell:	n/a	n/a
7	SMC3	chr3:52833128-52833423	GM12878	blood:	n/a	n/a
8	CTCF	chr3:52833300-52833450	AG04450	lung:	n/a	n/a
9	CTCF	chr3:52833162-52833394	MCF-7	breast:	n/a	chr3:52833256-52833274
10	CTCF	chr3:52833139-52833423	GM12878	blood:	n/a	chr3:52833256-52833274
11	CTCF	chr3:52833220-52833370	AG04450	lung:	n/a	chr3:52833256-52833274
12	CTCF	chr3:52833240-52833390	AoAF	blood vessel:	n/a	chr3:52833256-52833274
13	CTCF	chr3:52833155-52833377	A549	lung:	n/a	chr3:52833256-52833274
14	CTCF	chr3:52833136-52833378	H1-hESC	embryonic stem cell:	n/a	chr3:52833256-52833274
15	CTCF	chr3:52833138-52833379	GM19239	blood:	n/a	chr3:52833256-52833274
16	CTCF	chr3:52833220-52833370	AG10803	skin:	n/a	chr3:52833256-52833274
17	CTCF	chr3:52833220-52833370	BE2_C	brain:	n/a	chr3:52833256-52833274
18	SMC3	chr3:52833172-52833418	K562	blood:	n/a	n/a
19	MAFK	chr3:52833333-52833377	HepG2	liver:	n/a	n/a
20	CTCF	chr3:52833035-52833442	H1-hESC	embryonic stem cell:	n/a	chr3:52833256-52833274
21	CTCF	chr3:52833220-52833370	HCM	heart:	n/a	chr3:52833256-52833274
22	POLR2A	chr3:52833284-52833395	HepG2	liver:	n/a	n/a
23	CTCF	chr3:52832973-52833564	SK-N-SH	brain:	n/a	chr3:52833256-52833274
24	CTCF	chr3:52833130-52833405	K562	blood:	n/a	chr3:52833256-52833274
25	CTCF	chr3:52833141-52833383	MCF-7	breast:	n/a	chr3:52833256-52833274
26	CTCF	chr3:52833220-52833370	HCPEpiC	choroid plexus:	n/a	chr3:52833256-52833274
27	CTCF	chr3:52833240-52833390	HMEC	breast:	n/a	chr3:52833256-52833274
28	CTCF	chr3:52833091-52833416	GM19238	blood:	n/a	chr3:52833256-52833274
29	CTCF	chr3:52833070-52833404	GM12891	blood:	n/a	chr3:52833256-52833274
30	CTCF	chr3:52833160-52833413	HUVEC	blood vessel:	n/a	chr3:52833256-52833274
31	CTCF	chr3:52833220-52833370	SK-N-SH_RA	brain:	n/a	chr3:52833256-52833274
32	CTCF	chr3:52833158-52833385	GM10266	blood:	n/a	chr3:52833256-52833274
33	CTCF	chr3:52833220-52833370	HPF	lung:	n/a	chr3:52833256-52833274
34	RCOR1	chr3:52833149-52833382	K562	blood:	n/a	n/a
35	CTCF	chr3:52833173-52833367	MCF-7	breast:	n/a	chr3:52833256-52833274
36	ZNF143	chr3:52833108-52833437	H1-hESC	embryonic stem cell:	n/a	chr3:52833157-52833167
37	CTCF	chr3:52833240-52833390	AG09309	skin:	n/a	chr3:52833256-52833274
38	ZNF143	chr3:52833096-52833416	K562	blood:	n/a	chr3:52833157-52833167
39	SMC3	chr3:52833183-52833369	Hela-S3	cervix:	n/a	n/a
40	CTCF	chr3:52833079-52833465	K562	blood:	n/a	chr3:52833256-52833274
41	CTCF	chr3:52833146-52833400	HepG2	liver:	n/a	chr3:52833256-52833274
42	CTCF	chr3:52833220-52833370	GM12878	blood:	n/a	chr3:52833256-52833274
43	CTCF	chr3:52833151-52833390	Hela-S3	cervix:	n/a	chr3:52833256-52833274
44	RAD21	chr3:52832970-52833526	H1-hESC	embryonic stem cell:	n/a	chr3:52833254-52833273
45	CTCF	chr3:52833220-52833370	BJ	skin:	n/a	chr3:52833256-52833274
46	CTCF	chr3:52833093-52833409	K562	blood:	n/a	chr3:52833256-52833274
47	ZNF143	chr3:52833122-52833442	GM12878	blood:	n/a	chr3:52833157-52833167
48	RAD21	chr3:52833010-52833506	ECC-1	luminal epithelium:	n/a	chr3:52833254-52833273
49	RAD21	chr3:52833080-52833425	H1-hESC	embryonic stem cell:	n/a	chr3:52833254-52833273
50	POLR2A	chr3:52832743-52833470	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52831758..52833558-chr3:52833637..52835171,2	K562	blood:
2	chr3:52827101..52830669-chr3:52833208..52834941,3	K562	blood:
3	chr3:52803280..52805303-chr3:52832255..52833885,2	MCF-7	breast:
4	chr3:52831117..52833454-chr3:52835406..52839409,3	K562	blood:
5	chr3:52831402..52833454-chr3:52836536..52839409,2	K562	blood:
6	chr3:52719608..52722839-chr3:52830545..52833712,3	K562	blood:

Variant related genes	Relation type
ITIH3	TF binding region
ENSG00000163938	Chromatin interaction
ENSG00000162267	Chromatin interaction
ENSG00000163939	Chromatin interaction
ENSG00000114904	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking 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 target site	63 gene(s)	inside rSNPs	diseases
2	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer 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	27 gene(s)	inside rSNPs	diseases
4	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1010761	chr3:52804547-52851258	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	esv1810629	chr3:52817031-52869635	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv876797	chr3:52817675-52873984	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	esv3452194	chr3:52832512-52836010	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52825800-52836200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:52828200-52835800	Weak transcription	HSMMtube	muscle
3	chr3:52829000-52834200	Weak transcription	Brain Substantia Nigra	brain
4	chr3:52830400-52834000	Genic enhancers	HepG2	liver
5	chr3:52830400-52836400	Weak transcription	Pancreas	Pancrea
6	chr3:52830800-52835000	Genic enhancers	Liver	Liver
7	chr3:52832000-52833600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr3:52832800-52833600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:52833000-52833800	Weak transcription	Right Ventricle	heart
10	chr3:52833000-52833800	Weak transcription	Spleen	Spleen
11	chr3:52833000-52836200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:52833000-52836400	Weak transcription	HSMM	muscle
13	chr3:52833200-52834000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:52833200-52834000	Enhancers	Fetal Thymus	thymus
15	chr3:52833200-52835600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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