Variant report

Variant	rs5671
Chromosome Location	chr1:71512643-71512644
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	MAX	chr1:71512359-71513660	H1-hESC	embryonic stem cell:	n/a	chr1:71513532-71513542
2	POLR2A	chr1:71512040-71513854	K562	blood:	n/a	n/a
3	YY1	chr1:71512342-71513447	H1-hESC	embryonic stem cell:	n/a	chr1:71513364-71513375 chr1:71513412-71513426 chr1:71513421-71513432 chr1:71513329-71513340 chr1:71513328-71513337 chr1:71513322-71513336 chr1:71513360-71513371 chr1:71513319-71513333 chr1:71513423-71513437 chr1:71513426-71513435 chr1:71513423-71513432
4	E2F6	chr1:71512127-71513689	K562	blood:	n/a	chr1:71513534-71513543 chr1:71512854-71512869 chr1:71513390-71513400 chr1:71513430-71513440
5	MYC	chr1:71512553-71513293	MCF-7	breast:	n/a	n/a
6	MYC	chr1:71512002-71513714	K562	blood:	n/a	chr1:71513532-71513542
7	CTBP2	chr1:71512452-71513720	H1-hESC	embryonic stem cell:	n/a	n/a
8	MYC	chr1:71511963-71513739	K562	blood:	n/a	chr1:71513532-71513542
9	TEAD4	chr1:71512547-71512981	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr1:71512561-71512808	K562	blood:	n/a	n/a
11	POLR2A	chr1:71511962-71513787	K562	blood:	n/a	n/a
12	POLR2A	chr1:71512566-71513844	MCF-7	breast:	n/a	n/a
13	RCOR1	chr1:71512005-71513897	K562	blood:	n/a	n/a
14	UBTF	chr1:71511986-71513751	K562	blood:	n/a	n/a
15	CCNT2	chr1:71511971-71513807	K562	blood:	n/a	chr1:71513534-71513543 chr1:71512342-71512351
16	TBP	chr1:71511997-71513975	K562	blood:	n/a	n/a
17	YY1	chr1:71512598-71513650	K562	blood:	n/a	chr1:71513364-71513375 chr1:71513412-71513426 chr1:71513421-71513432 chr1:71513329-71513340 chr1:71513534-71513543 chr1:71513328-71513337 chr1:71513322-71513336 chr1:71513360-71513371 chr1:71513319-71513333 chr1:71513423-71513437 chr1:71513426-71513435 chr1:71513423-71513432
18	UBTF	chr1:71512011-71513650	K562	blood:	n/a	n/a
19	POLR2A	chr1:71511957-71513949	K562	blood:	n/a	n/a
20	TEAD4	chr1:71512642-71513229	K562	blood:	n/a	n/a
21	POLR2A	chr1:71510621-71513837	K562	blood:	n/a	n/a
22	POLR2A	chr1:71511798-71514436	SK-N-MC	brain:	n/a	n/a
23	E2F6	chr1:71512579-71512911	K562	blood:	n/a	chr1:71512854-71512869
24	E2F6	chr1:71512180-71513540	H1-hESC	embryonic stem cell:	n/a	chr1:71512854-71512869 chr1:71513390-71513400 chr1:71513430-71513440
25	HMGN3	chr1:71512175-71513739	K562	blood:	n/a	n/a
26	RCOR1	chr1:71512060-71512992	K562	blood:	n/a	n/a
27	MAX	chr1:71512532-71513635	SK-N-SH	brain:	n/a	chr1:71513532-71513542
28	MAX	chr1:71512280-71513676	H1-hESC	embryonic stem cell:	n/a	chr1:71513532-71513542
29	E2F6	chr1:71512104-71513672	H1-hESC	embryonic stem cell:	n/a	chr1:71513534-71513543 chr1:71512854-71512869 chr1:71513390-71513400 chr1:71513430-71513440
30	POLR2A	chr1:71511983-71513803	K562	blood:	n/a	n/a
31	POLR2A	chr1:71512577-71513756	K562	blood:	n/a	n/a
32	E2F6	chr1:71512150-71513678	K562	blood:	n/a	chr1:71513534-71513543 chr1:71512854-71512869 chr1:71513390-71513400 chr1:71513430-71513440
33	MAX	chr1:71512173-71513730	K562	blood:	n/a	chr1:71513532-71513542
34	MAZ	chr1:71512047-71513946	K562	blood:	n/a	chr1:71513532-71513542
35	MAX	chr1:71512005-71513709	K562	blood:	n/a	chr1:71513532-71513542
36	BHLHE40	chr1:71512038-71514051	K562	blood:	n/a	chr1:71513319-71513335 chr1:71513322-71513338 chr1:71513407-71513423 chr1:71513352-71513368 chr1:71513419-71513435
37	YY1	chr1:71512094-71513640	K562	blood:	n/a	chr1:71513364-71513375 chr1:71513412-71513426 chr1:71513421-71513432 chr1:71513329-71513340 chr1:71513534-71513543 chr1:71513328-71513337 chr1:71513322-71513336 chr1:71513360-71513371 chr1:71513319-71513333 chr1:71513423-71513437 chr1:71513426-71513435 chr1:71513423-71513432
38	JUND	chr1:71511931-71514040	K562	blood:	n/a	n/a
39	GTF2F1	chr1:71512564-71512785	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:71510894..71514340-chr1:71523075..71528309,6	K562	blood:
2	chr1:70994251..70996830-chr1:71512472..71514167,2	MCF-7	breast:
3	chr1:70978338..70980257-chr1:71510997..71512703,2	K562	blood:
4	chr1:71511577..71513859-chr1:71544920..71548466,4	K562	blood:
5	chr1:71113661..71115986-chr1:71510232..71513062,3	K562	blood:
6	chr1:71002710..71005624-chr1:71510534..71512998,2	K562	blood:
7	chr1:70876526..70879847-chr1:71510519..71513789,3	K562	blood:

Variant related genes	Relation type
ZRANB2-AS1	TF binding region
ENSG00000235079	Chromatin interaction
ENSG00000132485	Chromatin interaction
ENSG00000233020	Chromatin interaction
ENSG00000116761	Chromatin interaction
ENSG00000229956	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10128001	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10493483	0.82[AMR][1000 genomes]
rs10518356	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11556475	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13376594	0.82[EUR][1000 genomes]
rs17090802	0.80[CEU][hapmap];0.97[EUR][1000 genomes]
rs17090808	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs17090932	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs17091001	0.82[AMR][1000 genomes]
rs17091015	0.85[AMR][1000 genomes]
rs17091024	0.82[AMR][1000 genomes]
rs17091028	0.85[AMR][1000 genomes]
rs2050066	1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs41287936	1.00[EUR][1000 genomes]
rs5673	0.97[EUR][1000 genomes]
rs56752457	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5676	0.97[EUR][1000 genomes]
rs5691	1.00[ASW][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs58163483	0.94[EUR][1000 genomes]
rs58281678	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58293304	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59834169	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60078028	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs726352	0.82[AMR][1000 genomes]
rs74087222	0.82[EUR][1000 genomes]
rs74090259	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7531741	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7552415	1.00[CEU][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1845198	chr1:71274759-71514969	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv546472	chr1:71432984-71541003	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	555 gene(s)	inside rSNPs	diseases
3	esv1850593	chr1:71444149-71514969	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv871242	chr1:71481050-71519326	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:71510600-71513800	Active TSS	Aorta	Aorta
2	chr1:71510600-71514000	Active TSS	NHDF-Ad	bronchial
3	chr1:71510800-71514200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr1:71511000-71513600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
5	chr1:71511000-71514000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
6	chr1:71511000-71514200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:71511000-71514400	Bivalent/Poised TSS	Fetal Kidney	kidney
8	chr1:71511400-71513400	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
9	chr1:71511400-71514200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:71512000-71512800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:71512000-71513000	Bivalent Enhancer	Fetal Brain Male	brain
12	chr1:71512000-71513000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
13	chr1:71512000-71513200	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
14	chr1:71512000-71513200	Flanking Bivalent TSS/Enh	Placenta	Placenta
15	chr1:71512000-71513800	Flanking Active TSS	Right Ventricle	heart
16	chr1:71512000-71514000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:71512000-71514000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
18	chr1:71512000-71514000	Bivalent/Poised TSS	NHLF	lung
19	chr1:71512200-71512800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
20	chr1:71512200-71512800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr1:71512200-71512800	Flanking Bivalent TSS/Enh	Primary T helper naive cells from peripheral blood	blood
22	chr1:71512200-71512800	Flanking Bivalent TSS/Enh	Esophagus	oesophagus
23	chr1:71512200-71512800	Bivalent Enhancer	Fetal Thymus	thymus
24	chr1:71512200-71512800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
25	chr1:71512200-71513000	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
26	chr1:71512200-71513000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
27	chr1:71512200-71513200	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:71512200-71513200	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
29	chr1:71512200-71513200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
30	chr1:71512200-71513200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
31	chr1:71512200-71513600	Flanking Active TSS	Pancreas	Pancrea
32	chr1:71512200-71513800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
33	chr1:71512200-71513800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
34	chr1:71512200-71513800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
35	chr1:71512200-71513800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
36	chr1:71512200-71514000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
37	chr1:71512200-71514000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:71512200-71514000	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr1:71512200-71514000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
40	chr1:71512200-71514000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
41	chr1:71512400-71512800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:71512400-71512800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:71512400-71512800	Bivalent Enhancer	Liver	Liver
44	chr1:71512400-71512800	Active TSS	Fetal Heart	heart
45	chr1:71512400-71512800	Flanking Active TSS	Gastric	stomach
46	chr1:71512400-71512800	Bivalent Enhancer	HUVEC	blood vessel
47	chr1:71512400-71512800	Flanking Active TSS	K562	blood
48	chr1:71512400-71513000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
49	chr1:71512400-71513000	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 2	blood
50	chr1:71512400-71513000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain

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