Variant report

Variant	rs13398175
Chromosome Location	chr2:173378821-173378822
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	SPI1	chr2:173378584-173379281	HL-60	blood:	n/a	chr2:173379222-173379235 chr2:173379052-173379065 chr2:173379055-173379062
2	ATF1	chr2:173378585-173378961	K562	blood:	n/a	n/a
3	JUND	chr2:173378642-173379102	K562	blood:	n/a	n/a
4	MYC	chr2:173378291-173379439	NB4	blood:	n/a	n/a
5	SPI1	chr2:173378628-173378870	K562	blood:	n/a	n/a
6	HCFC1	chr2:173378751-173378851	K562	blood:	n/a	n/a
7	IRF1	chr2:173378626-173378877	K562	blood:	n/a	n/a
8	POLR2A	chr2:173378240-173379529	HL-60	blood:	n/a	n/a
9	GATA1	chr2:173378345-173379409	PBDE	blood:	n/a	n/a
10	MAX	chr2:173378290-173379433	NB4	blood:	n/a	n/a
11	MAFF	chr2:173378783-173379017	K562	blood:	n/a	n/a
12	TAL1	chr2:173378669-173378968	K562	blood:	n/a	n/a
13	MAZ	chr2:173378699-173378855	K562	blood:	n/a	n/a
14	MAX	chr2:173378750-173378950	K562	blood:	n/a	n/a
15	GATA1	chr2:173378396-173379244	K562	blood:	n/a	n/a
16	GATA2	chr2:173378659-173378958	K562	blood:	n/a	n/a
17	TEAD4	chr2:173378547-173378994	K562	blood:	n/a	n/a
18	CEBPD	chr2:173378576-173378959	K562	blood:	n/a	n/a
19	BHLHE40	chr2:173378645-173378970	K562	blood:	n/a	n/a
20	RCOR1	chr2:173378277-173379015	K562	blood:	n/a	n/a
21	REST	chr2:173378641-173379534	HL-60	blood:	n/a	n/a
22	POLR2A	chr2:173378184-173379400	HL-60	blood:	n/a	n/a
23	CCNT2	chr2:173378653-173378938	K562	blood:	n/a	n/a
24	POLR2A	chr2:173378434-173379432	NB4	blood:	n/a	n/a
25	SPI1	chr2:173378479-173379437	HL-60	blood:	n/a	chr2:173379222-173379235 chr2:173379052-173379065 chr2:173379055-173379062
26	ZNF384	chr2:173378647-173379086	K562	blood:	n/a	n/a
27	EP300	chr2:173378611-173378999	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173378812..173379330-chr2:173420697..173421245,2	NB4	blood:
2	chr2:173378324..173380878-chr2:173382092..173384588,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225205	TF binding region
ENSG00000225205	Chromatin interaction
ENSG00000152256	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10174809	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs12052479	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12469537	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1574257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34871211	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35022330	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3792259	0.83[YRI][hapmap]
rs4075604	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55966259	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56832945	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61194385	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6730763	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7562753	0.81[EUR][1000 genomes]
rs7562865	0.81[EUR][1000 genomes]
rs7596665	0.81[YRI][hapmap]

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	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173356400-173379200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:173372600-173379600	Enhancers	Primary B cells from peripheral blood	blood
3	chr2:173375000-173380800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:173375400-173379200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:173376000-173379000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
6	chr2:173376400-173397400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:173377200-173386000	Weak transcription	Primary T cells from cord blood	blood
8	chr2:173377400-173380800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:173378200-173379000	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr2:173378200-173379400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:173378200-173379600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr2:173378200-173380000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:173378600-173379200	Flanking Active TSS	K562	blood
14	chr2:173378600-173383400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:173378800-173379000	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr2:173378800-173379400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr2:173378800-173379400	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr2:173378800-173379600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links