Variant report

Variant	rs3402
Chromosome Location	chr1:161135421-161135422
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:62)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:62 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:161135317-161136363	K562	blood:	n/a	chr1:161135864-161135877
2	SP1	chr1:161135341-161136727	HCT-116	colon:	n/a	n/a
3	HCFC1	chr1:161135197-161137330	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr1:161135398-161136407	GM12878	blood:	n/a	chr1:161135864-161135877
5	POLR2A	chr1:161134838-161136525	PFSK-1	brain:	n/a	n/a
6	RAD21	chr1:161135414-161135767	SK-N-SH_RA	brain:	n/a	n/a
7	POLR2A	chr1:161135354-161137285	K562	blood:	n/a	n/a
8	PML	chr1:161135392-161137068	K562	blood:	n/a	n/a
9	GATA1	chr1:161135364-161137128	PBDE	blood:	n/a	chr1:161135693-161135703 chr1:161135759-161135768
10	FOXM1	chr1:161135419-161136817	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:161135364-161137021	K562	blood:	n/a	n/a
12	POLR2A	chr1:161135397-161136505	PANC-1	pancreas:	n/a	n/a
13	SP1	chr1:161135419-161136645	A549	lung:	n/a	n/a
14	PML	chr1:161135302-161136941	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:161135396-161136639	U87	brain:	n/a	n/a
16	FOXM1	chr1:161135417-161136469	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:161134767-161137577	K562	blood:	n/a	n/a
18	SP1	chr1:161135419-161136557	A549	lung:	n/a	n/a
19	TEAD4	chr1:161135380-161137125	K562	blood:	n/a	n/a
20	POLR2A	chr1:161134943-161136740	K562	blood:	n/a	n/a
21	POLR2A	chr1:161134880-161137092	Hela-S3	cervix:	n/a	n/a
22	CTCF	chr1:161135388-161135766	HepG2	liver:	n/a	n/a
23	POLR2A	chr1:161135343-161136633	HUVEC	blood vessel:	n/a	n/a
24	CBX3	chr1:161135411-161137122	K562	blood:	n/a	n/a
25	CTCF	chr1:161135388-161135763	H1-hESC	embryonic stem cell:	n/a	n/a
26	TCF12	chr1:161135330-161136728	A549	lung:	n/a	n/a
27	ZMIZ1	chr1:161135389-161136855	K562	blood:	n/a	n/a
28	CTCF	chr1:161135334-161136211	MCF-7	breast:	n/a	chr1:161135864-161135877
29	POLR2A	chr1:161134954-161137237	PBDE	blood:	n/a	n/a
30	POLR2A	chr1:161134654-161137060	MCF10A-Er-Src	breast:	n/a	n/a
31	REST	chr1:161135344-161136959	H1-neurons	neurons:	n/a	chr1:161135846-161135854
32	POLR2A	chr1:161134747-161136646	SK-N-MC	brain:	n/a	n/a
33	CTCF	chr1:161135367-161136217	K562	blood:	n/a	chr1:161135864-161135877
34	POLR2A	chr1:161135156-161137337	IMR90	lung:	n/a	n/a
35	POLR2A	chr1:161135104-161136892	MCF10A-Er-Src	breast:	n/a	n/a
36	CTCF	chr1:161135417-161135736	SK-N-SH_RA	brain:	n/a	n/a
37	MTA3	chr1:161135400-161136961	GM12878	blood:	n/a	n/a
38	MAX	chr1:161135379-161136921	A549	lung:	n/a	n/a
39	CTCF	chr1:161135392-161136516	K562	blood:	n/a	chr1:161135864-161135877
40	ATF2	chr1:161135417-161136481	GM12878	blood:	n/a	n/a
41	POLR2A	chr1:161135390-161136645	U87	brain:	n/a	n/a
42	GATA1	chr1:161134959-161137227	K562	blood:	n/a	chr1:161135055-161135065 chr1:161135693-161135703 chr1:161135759-161135768
43	TAF1	chr1:161135420-161136572	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr1:161135405-161136987	Hela-S3	cervix:	n/a	n/a
45	FOSL2	chr1:161135280-161136615	A549	lung:	n/a	n/a
46	POLR2A	chr1:161135414-161137022	K562	blood:	n/a	n/a
47	MXI1	chr1:161135310-161137378	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr1:161134823-161136817	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr1:161135414-161136996	HL-60	blood:	n/a	n/a
50	POLR2A	chr1:161135327-161137239	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:161099668..161103758-chr1:161134918..161138367,5	MCF-7	breast:
2	chr1:161100027..161102916-chr1:161132751..161137101,5	K562	blood:
3	chr1:161086949..161089395-chr1:161134747..161137999,5	K562	blood:
4	chr1:161133675..161135632-chr20:45893847..45895708,2	MCF-7	breast:
5	chr1:161085942..161091087-chr1:161134747..161138869,10	K562	blood:
6	chr1:161040956..161045180-chr1:161134527..161136918,3	MCF-7	breast:
7	chr1:161135373..161143326-chr1:161144272..161149580,16	MCF-7	breast:
8	chr1:161133737..161136347-chr1:161193972..161196200,2	K562	blood:
9	chr1:161100027..161103465-chr1:161134887..161137955,5	K562	blood:
10	chr1:161086404..161089001-chr1:161134756..161136300,2	MCF-7	breast:

No data

Variant related genes	Relation type
PPOX	TF binding region
ENSG00000158882	Chromatin interaction
ENSG00000143256	Chromatin interaction
ENSG00000158850	Chromatin interaction
ENSG00000143217	Chromatin interaction
ENSG00000158796	Chromatin interaction
ENSG00000158793	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11576415	0.83[AFR][1000 genomes]
rs11583589	0.83[AFR][1000 genomes]
rs11590967	0.83[AFR][1000 genomes]
rs12077004	1.00[ASW][hapmap]
rs6413453	1.00[ASW][hapmap]
rs72714913	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72714915	0.87[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161130000-161135600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:161132400-161135600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:161133400-161135600	Weak transcription	Small Intestine	intestine
4	chr1:161134000-161135600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:161134400-161135600	Weak transcription	Gastric	stomach
6	chr1:161134800-161135600	Enhancers	Fetal Heart	heart
7	chr1:161134800-161135800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:161134800-161135800	Transcr. at gene 5' and 3'	K562	blood
9	chr1:161135000-161135600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:161135000-161135600	Enhancers	Primary hematopoietic stem cells	blood
11	chr1:161135000-161135800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:161135000-161135800	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr1:161135000-161136000	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr1:161135000-161136000	Flanking Active TSS	Dnd41	blood
15	chr1:161135000-161136400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:161135000-161137200	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr1:161135000-161137200	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr1:161135000-161137400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:161135000-161137400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:161135200-161135600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:161135200-161135600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:161135200-161135600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:161135200-161135600	Enhancers	Fetal Brain Male	brain
24	chr1:161135200-161135600	Enhancers	Fetal Lung	lung
25	chr1:161135200-161135600	Enhancers	Spleen	Spleen
26	chr1:161135200-161135600	Flanking Active TSS	GM12878-XiMat	blood
27	chr1:161135200-161135600	Flanking Active TSS	HSMMtube	muscle
28	chr1:161135200-161135800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:161135200-161135800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
30	chr1:161135200-161135800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr1:161135200-161135800	Flanking Active TSS	Fetal Brain Female	brain
32	chr1:161135200-161135800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
33	chr1:161135200-161135800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
34	chr1:161135200-161135800	Active TSS	HepG2	liver
35	chr1:161135200-161135800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr1:161135200-161135800	Flanking Active TSS	NHEK	skin
37	chr1:161135200-161136000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr1:161135200-161136000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:161135200-161136000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr1:161135200-161136000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:161135200-161136000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:161135200-161136000	Flanking Active TSS	Liver	Liver
43	chr1:161135200-161136000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr1:161135200-161136400	Active TSS	Primary T cells from cord blood	blood
45	chr1:161135200-161136800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:161135200-161137000	Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr1:161135200-161137400	Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr1:161135200-161137400	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr1:161135200-161137400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr1:161135200-161137400	Active TSS	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links