Variant report

Variant	rs4382171
Chromosome Location	chr5:17399509-17399510
allele	C/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	chr5:17398812-17400352	HL-60	blood:	n/a	chr5:17399218-17399227 chr5:17400267-17400280

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:17399274..17401360-chr5:17404322..17406946,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248455	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12654414	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13178605	0.89[ASN][1000 genomes]
rs1500506	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1500507	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972037	0.95[CEU][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2008011	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2055875	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34875290	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35497365	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4701683	0.89[ASN][1000 genomes]
rs4701684	0.90[ASN][1000 genomes]
rs4701685	0.90[ASN][1000 genomes]
rs4702207	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs4702208	0.90[ASN][1000 genomes]
rs58439032	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6554994	0.87[ASN][1000 genomes]
rs6554995	0.87[ASN][1000 genomes]
rs6554996	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6554997	0.89[ASN][1000 genomes]
rs6554998	0.90[ASN][1000 genomes]
rs6876143	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6887129	0.89[ASN][1000 genomes]
rs6892106	0.89[ASN][1000 genomes]
rs7704602	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7704923	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7705370	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7705848	0.89[ASN][1000 genomes]
rs7706156	0.89[ASN][1000 genomes]
rs7727410	0.90[ASN][1000 genomes]
rs7730990	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs867356	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs964751	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs964752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029959	chr5:17133214-17455995	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	nsv461988	chr5:17296342-17484038	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv597313	chr5:17296342-17484038	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv830219	chr5:17325802-17518914	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	esv1793466	chr5:17364700-17721569	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
6	esv1801170	chr5:17364700-17721569	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
7	esv1820519	chr5:17364700-17721569	Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
8	esv1824831	chr5:17364700-17721569	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
9	esv1827359	chr5:17364700-17721569	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
10	esv1828062	chr5:17364700-17721569	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
11	nsv427713	chr5:17364700-17721569	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
12	nsv428464	chr5:17364700-17721569	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
13	esv2757986	chr5:17364700-17936404	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
14	esv2759328	chr5:17364700-17936404	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
15	nsv1017469	chr5:17373383-17416643	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	n/a
16	nsv980966	chr5:17379819-17496300	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv1023600	chr5:17382604-17418330	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv1031214	chr5:17382604-17427825	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
19	nsv881474	chr5:17390145-17509888	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
20	nsv968881	chr5:17391605-17484624	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
21	esv2757108	chr5:17398090-17804346	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
22	nsv1030762	chr5:17398399-17690362	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:17396400-17400000	Weak transcription	Placenta	Placenta
2	chr5:17396600-17400800	Weak transcription	Fetal Kidney	kidney
3	chr5:17396800-17399600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:17397200-17401600	Enhancers	Primary B cells from peripheral blood	blood
5	chr5:17397400-17400800	Weak transcription	Ovary	ovary
6	chr5:17397600-17402000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr5:17397800-17399600	Enhancers	NH-A	brain
8	chr5:17397800-17401000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:17397800-17403000	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr5:17398000-17399600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:17398000-17399600	Enhancers	HSMM	muscle
12	chr5:17398000-17399600	Enhancers	NHDF-Ad	bronchial
13	chr5:17398000-17399600	Enhancers	NHEK	skin
14	chr5:17398000-17400200	Enhancers	Primary hematopoietic stem cells	blood
15	chr5:17398000-17400800	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr5:17398000-17400800	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr5:17398200-17399600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
18	chr5:17398200-17400600	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr5:17398200-17400800	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr5:17398400-17399600	Enhancers	GM12878-XiMat	blood
21	chr5:17398400-17400600	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr5:17398600-17403000	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr5:17398800-17399600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr5:17398800-17401000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr5:17398800-17401000	Enhancers	Primary B cells from cord blood	blood
26	chr5:17399000-17399800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr5:17399000-17400800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr5:17399000-17401000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:17399000-17401400	Weak transcription	Hela-S3	cervix
30	chr5:17399000-17402200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr5:17399000-17402400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr5:17399200-17399600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
33	chr5:17399200-17399600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr5:17399200-17400800	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr5:17399200-17400800	Weak transcription	A549	lung
36	chr5:17399200-17402400	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr5:17399400-17400200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
38	chr5:17399400-17401400	Weak transcription	HSMMtube	muscle
39	chr5:17399400-17405800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr5:17399400-17406200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links