Variant report

Variant	rs309926
Chromosome Location	chr5:42971700-42971701
allele	G/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	CEBPB	chr5:42971655-42972202	HepG2	liver:	n/a	chr5:42971763-42971774 chr5:42971763-42971776 chr5:42972033-42972044 chr5:42971763-42971776
2	CTCF	chr5:42971640-42971790	BJ	skin:	n/a	n/a
3	CTCF	chr5:42971178-42971705	K562	blood:	n/a	chr5:42971442-42971458 chr5:42971441-42971459
4	CTCF	chr5:42971228-42971883	A549	lung:	n/a	chr5:42971442-42971458 chr5:42971441-42971459
5	CTCF	chr5:42971093-42971742	HCT-116	colon:	n/a	chr5:42971442-42971458 chr5:42971441-42971459
6	CEBPB	chr5:42971693-42972171	IMR90	lung:	n/a	chr5:42971763-42971774 chr5:42971763-42971776 chr5:42972033-42972044 chr5:42971763-42971776
7	RAD21	chr5:42971090-42971784	HCT-116	colon:	n/a	chr5:42971439-42971458 chr5:42971441-42971453 chr5:42971442-42971455
8	ELF1	chr5:42971307-42971717	K562	blood:	n/a	chr5:42971504-42971517 chr5:42971506-42971517 chr5:42971506-42971517
9	RAD21	chr5:42971107-42971700	H1-hESC	embryonic stem cell:	n/a	chr5:42971439-42971458 chr5:42971441-42971453 chr5:42971442-42971455
10	RAD21	chr5:42971284-42971774	MCF-7	breast:	n/a	chr5:42971439-42971458 chr5:42971441-42971453 chr5:42971442-42971455

No.	Distal block	Cell Line	Cell type
1	chr5:42969037..42971723-chr5:42975649..42977780,2	K562	blood:
2	chr5:42911987..42912980-chr5:42970878..42972001,4	MCF-7	breast:
3	chr1:149857438..149858970-chr5:42971662..42973369,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C5orf39-7	chr5:42971231-42971776	NONHSAT101239

Variant related genes	Relation type
ENSG00000250711	TF binding region
ENSG00000184260	Chromatin interaction
ENSG00000184678	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10036916	0.92[ASN][1000 genomes]
rs10064003	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10522	0.83[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10941604	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10941605	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11747435	0.87[ASN][1000 genomes]
rs11747714	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11958008	0.87[ASN][1000 genomes]
rs12697439	0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13169690	0.83[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13170208	0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs13178479	0.81[ASN][1000 genomes]
rs13179934	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1542369	0.89[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs1574407	0.89[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap]
rs160709	0.83[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1618891	0.85[JPT][hapmap]
rs1624415	0.85[JPT][hapmap]
rs178415	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs186323	0.99[ASN][1000 genomes]
rs186324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1902101	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2100473	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2124069	0.84[AMR][1000 genomes]
rs222060	0.83[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2247280	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2253450	0.87[ASN][1000 genomes]
rs2329994	0.84[AMR][1000 genomes]
rs2329995	0.89[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2548334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2548336	0.88[CHB][hapmap];0.88[ASN][1000 genomes]
rs2548339	0.99[ASN][1000 genomes]
rs2548341	0.96[ASN][1000 genomes]
rs2548343	0.97[ASN][1000 genomes]
rs2548345	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548346	0.95[ASN][1000 genomes]
rs2548349	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2548350	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2548353	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2548356	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2548373	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2603620	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2603634	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2603644	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2603651	0.87[ASN][1000 genomes]
rs2603656	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2876993	0.82[ASN][1000 genomes]
rs2882295	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2924817	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs309909	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs309914	0.83[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs309921	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs309922	0.96[ASN][1000 genomes]
rs309923	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs309924	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309948	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs309950	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[ASN][1000 genomes]
rs315262	0.86[CEU][hapmap]
rs316395	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs316404	0.83[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap]
rs316408	0.83[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap]
rs316413	0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap]
rs316414	0.89[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs316416	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs316419	0.85[AMR][1000 genomes]
rs316422	0.85[AMR][1000 genomes]
rs3849697	0.92[ASN][1000 genomes]
rs3893725	0.82[ASN][1000 genomes]
rs3909456	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4033115	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4092293	0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4092294	0.83[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4296812	0.89[AMR][1000 genomes]
rs512921	0.86[JPT][hapmap]
rs557076	0.85[JPT][hapmap]
rs567884	0.85[JPT][hapmap]
rs613825	0.85[AMR][1000 genomes]
rs643307	0.84[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6451660	0.83[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6451661	0.83[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6451662	0.89[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6875214	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6879130	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs6880163	0.91[ASN][1000 genomes]
rs6882794	0.88[ASN][1000 genomes]
rs6883097	0.93[ASN][1000 genomes]
rs6892422	0.85[JPT][hapmap]
rs6899257	0.92[ASN][1000 genomes]
rs724430	0.90[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs768441	0.84[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7707797	0.88[ASN][1000 genomes]
rs7715065	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7733383	0.92[ASN][1000 genomes]
rs782971	0.85[JPT][hapmap]
rs782978	0.85[JPT][hapmap]
rs903391	0.86[JPT][hapmap]
rs9292862	0.83[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
7	nsv1018276	chr5:42809131-42975245	Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	esv1813779	chr5:42906572-42992040	Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv1029288	chr5:42928085-43047323	Flanking Bivalent TSS/Enh Active TSS Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	120 gene(s)	inside rSNPs	diseases
10	nsv1020910	chr5:42929799-43000021	Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	nsv537738	chr5:42929799-43000021	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
12	nsv968169	chr5:42956713-43043472	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	116 gene(s)	inside rSNPs	diseases
13	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
14	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
15	nsv881436	chr5:42967215-43008917	Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
16	nsv880447	chr5:42967215-43030798	Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42954800-42982200	Weak transcription	HUVEC	blood vessel
2	chr5:42955000-42972600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr5:42962200-42984400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr5:42966400-42974600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr5:42966600-42972000	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr5:42966600-42972400	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr5:42966800-42972200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr5:42967000-42985600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr5:42967400-42972200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:42969400-42985400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr5:42970400-42972200	Weak transcription	Thymus	Thymus
12	chr5:42970400-42974600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:42970600-42973600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:42970600-42977600	Weak transcription	Spleen	Spleen
15	chr5:42970800-42973600	Weak transcription	Primary T cells from cord blood	blood
16	chr5:42970800-42988400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr5:42971000-42982400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:42971000-42984400	Weak transcription	Primary B cells from cord blood	blood
19	chr5:42971000-42985400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr5:42971200-42971800	Enhancers	Placenta	Placenta
21	chr5:42971400-42972200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr5:42971400-42973600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr5:42971400-42979200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links