Variant report

Variant	rs56343901
Chromosome Location	chr1:209958659-209958660
allele	A/G
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	POLR2A	chr1:209957624-209958689	GM12891	blood:	n/a	n/a
2	POLR2A	chr1:209954531-209958662	K562	blood:	n/a	n/a
3	POLR2A	chr1:209958625-209958676	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr1:209957453-209958705	GM12892	blood:	n/a	n/a
5	CBX3	chr1:209957472-209958679	K562	blood:	n/a	chr1:209957492-209957503
6	POLR2A	chr1:209957498-209958933	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:209957405-209958850	PBDE	blood:	n/a	n/a
8	POLR2A	chr1:209952928-209958954	GM12878	blood:	n/a	n/a
9	KAP1	chr1:209958006-209958905	K562	blood:	n/a	n/a
10	MAX	chr1:209957393-209958662	A549	lung:	n/a	chr1:209957805-209957814
11	HCFC1	chr1:209957118-209958766	Hela-S3	cervix:	n/a	n/a
12	USF2	chr1:209957412-209958746	GM12878	blood:	n/a	n/a
13	E2F6	chr1:209957426-209958677	A549	lung:	n/a	chr1:209958132-209958139 chr1:209957943-209957952 chr1:209958132-209958139 chr1:209957593-209957603 chr1:209957945-209957954 chr1:209958132-209958139 chr1:209957899-209957908
14	IRF1	chr1:209957279-209958673	K562	blood:	n/a	chr1:209957594-209957608 chr1:209957344-209957358
15	POLR2A	chr1:209956778-209958666	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr1:209957465-209958681	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr1:209952746-209958845	GM12891	blood:	n/a	n/a
18	JUND	chr1:209957239-209958696	SK-N-SH	brain:	n/a	chr1:209957944-209957953
19	MTA3	chr1:209957181-209958688	GM12878	blood:	n/a	n/a
20	ZNF384	chr1:209957511-209958666	K562	blood:	n/a	n/a
21	JUN	chr1:209957166-209959100	K562	blood:	n/a	chr1:209957194-209957206 chr1:209957943-209957956 chr1:209957944-209957953

No.	Distal block	Cell Line	Cell type
1	chr1:209955222..209959394-chr1:210545816..210547914,4	K562	blood:
2	chr1:209946631..209949857-chr1:209956266..209959109,3	MCF-7	breast:
3	chr1:209955520..209962214-chr1:209976009..209982555,8	K562	blood:
4	chr1:209940429..209942619-chr1:209957623..209959222,2	MCF-7	breast:
5	chr1:209957348..209959526-chr1:209965730..209967837,2	K562	blood:
6	chr1:209950429..209953463-chr1:209956092..209959569,7	K562	blood:
7	chr1:209957965..209959806-chr1:209959959..209962744,2	K562	blood:
8	chr1:209954505..209956563-chr1:209958183..209960148,2	K562	blood:
9	chr1:209957266..209960368-chr1:209964452..209967778,3	MCF-7	breast:
10	chr1:209955602..209959674-chr1:209962858..209967873,6	MCF-7	breast:
11	chr1:209956289..209959543-chr1:209978892..209981541,4	K562	blood:
12	chr1:209958606..209961246-chr1:209973550..209976119,2	MCF-7	breast:

Variant related genes	Relation type
C1orf74	TF binding region
ENSG00000009790	Chromatin interaction
ENSG00000200972	Chromatin interaction
ENSG00000232222	Chromatin interaction
ENSG00000117595	Chromatin interaction

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	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv4343	chr1:209929932-209974877	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1067914	chr1:209955818-209972979	Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
7	nsv945273	chr1:209958252-209960036	Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209957200-209958800	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr1:209957800-209978600	Weak transcription	Spleen	Spleen
3	chr1:209958000-209958800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr1:209958000-209958800	Flanking Active TSS	Dnd41	blood
5	chr1:209958000-209960600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:209958000-209961000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:209958000-209961400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:209958000-209971600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:209958200-209958800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:209958200-209959000	ZNF genes & repeats	K562	blood
11	chr1:209958200-209959200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
12	chr1:209958200-209962600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:209958200-209963800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:209958400-209958800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr1:209958400-209958800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:209958400-209958800	Enhancers	Fetal Thymus	thymus
17	chr1:209958400-209959000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:209958400-209959400	Genic enhancers	HMEC	breast
19	chr1:209958400-209960200	Weak transcription	Right Atrium	heart
20	chr1:209958400-209960600	Enhancers	Liver	Liver
21	chr1:209958400-209960800	Enhancers	Left Ventricle	heart
22	chr1:209958400-209961800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr1:209958400-209962200	Weak transcription	Esophagus	oesophagus
24	chr1:209958400-209962200	Enhancers	Pancreatic Islets	Pancreatic Islet
25	chr1:209958400-209962400	Enhancers	Stomach Mucosa	stomach
26	chr1:209958400-209962800	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr1:209958400-209968600	Weak transcription	Lung	lung
28	chr1:209958400-209971800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:209958400-209974000	Weak transcription	Aorta	Aorta
30	chr1:209958400-209978600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:209958600-209958800	Enhancers	Primary B cells from cord blood	blood
32	chr1:209958600-209958800	Enhancers	Primary B cells from peripheral blood	blood
33	chr1:209958600-209958800	Enhancers	Primary T cells from cord blood	blood
34	chr1:209958600-209958800	Enhancers	Primary T cells fromperipheralblood	blood
35	chr1:209958600-209958800	Active TSS	Primary hematopoietic stem cells	blood
36	chr1:209958600-209958800	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr1:209958600-209958800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:209958600-209958800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr1:209958600-209958800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr1:209958600-209958800	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr1:209958600-209958800	Enhancers	Small Intestine	intestine
42	chr1:209958600-209958800	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr1:209958600-209959000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr1:209958600-209959000	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr1:209958600-209959000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr1:209958600-209959000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr1:209958600-209959000	Enhancers	Fetal Heart	heart
48	chr1:209958600-209959400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:209958600-209959600	Weak transcription	Colon Smooth Muscle	Colon
50	chr1:209958600-209959600	Strong transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links