Variant report

Variant	rs2242412
Chromosome Location	chr5:1801689-1801690
allele	A/C
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	JUND	chr5:1799770-1802111	K562	blood:	n/a	chr5:1799990-1799999 chr5:1799987-1799996 chr5:1800154-1800168 chr5:1799991-1800000 chr5:1799988-1799997
2	RCOR1	chr5:1799791-1801796	Hela-S3	cervix:	n/a	n/a
3	SMARCC2	chr5:1799899-1801839	Hela-S3	cervix:	n/a	n/a
4	TBP	chr5:1799280-1802309	K562	blood:	n/a	n/a
5	CTCF	chr5:1801680-1801830	SK-N-SH_RA	brain:	n/a	chr5:1801687-1801700
6	POLR2A	chr5:1799337-1802213	K562	blood:	n/a	n/a
7	POLR2A	chr5:1801157-1801876	A549	lung:	n/a	n/a
8	STAT5A	chr5:1800706-1801854	GM12878	blood:	n/a	n/a
9	POLR2A	chr5:1799154-1802375	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr5:1801291-1801871	HUVEC	blood vessel:	n/a	n/a
11	MAX	chr5:1799413-1801875	HepG2	liver:	n/a	chr5:1800000-1800009 chr5:1800776-1800789 chr5:1799998-1800011 chr5:1800779-1800788 chr5:1799988-1799998 chr5:1800776-1800789 chr5:1799999-1800010 chr5:1799985-1799995 chr5:1800778-1800787 chr5:1800000-1800009 chr5:1800778-1800787 chr5:1800777-1800788 chr5:1800777-1800788 chr5:1800778-1800787
12	HA-E2F1	chr5:1799960-1802245	MCF-7	breast:	n/a	chr5:1801422-1801431 chr5:1801419-1801431 chr5:1801475-1801484 chr5:1800052-1800061 chr5:1801454-1801461 chr5:1801453-1801462 chr5:1799984-1799993
13	E2F6	chr5:1801155-1801748	K562	blood:	n/a	chr5:1801422-1801431 chr5:1801419-1801431 chr5:1801475-1801484 chr5:1801454-1801461 chr5:1801453-1801462
14	NR2C2	chr5:1801296-1801897	GM12878	blood:	n/a	chr5:1801506-1801521 chr5:1801510-1801519 chr5:1801508-1801521 chr5:1801401-1801410
15	POLR2A	chr5:1801191-1801843	Gliobla	brain:	n/a	n/a
16	EP300	chr5:1801514-1801714	GM12878	blood:	n/a	n/a
17	PML	chr5:1801090-1801825	K562	blood:	n/a	n/a
18	POLR2A	chr5:1801161-1801937	U87	brain:	n/a	n/a
19	CHD1	chr5:1799337-1802013	GM12878	blood:	n/a	chr5:1801420-1801430
20	POLR2A	chr5:1801081-1802302	K562	blood:	n/a	n/a
21	POLR2A	chr5:1801267-1801773	HUVEC	blood vessel:	n/a	n/a
22	YY1	chr5:1801272-1801865	SK-N-SH_RA	brain:	n/a	chr5:1801527-1801539 chr5:1801422-1801431
23	ZBTB7A	chr5:1801300-1801829	K562	blood:	n/a	n/a
24	TAF1	chr5:1801371-1801999	K562	blood:	n/a	n/a
25	SMARCC1	chr5:1800159-1802268	Hela-S3	cervix:	n/a	n/a
26	GTF2F1	chr5:1801062-1801729	H1-hESC	embryonic stem cell:	n/a	n/a
27	TBP	chr5:1799787-1802268	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr5:1799089-1802204	HepG2	liver:	n/a	n/a
29	ZNF274	chr5:1801460-1801926	K562	blood:	n/a	n/a
30	E2F4	chr5:1801166-1801716	K562	blood:	n/a	chr5:1801422-1801431 chr5:1801419-1801431 chr5:1801475-1801484 chr5:1801454-1801461 chr5:1801453-1801462
31	TEAD4	chr5:1799783-1801813	K562	blood:	n/a	n/a
32	POLR2A	chr5:1799155-1802340	Hela-S3	cervix:	n/a	n/a
33	SIN3AK20	chr5:1801181-1801903	HepG2	liver:	n/a	n/a
34	TCF12	chr5:1801107-1801963	ECC-1	luminal epithelium:	n/a	chr5:1801701-1801708
35	NR2F2	chr5:1801109-1801917	K562	blood:	n/a	chr5:1801506-1801521
36	CTCF	chr5:1801600-1801750	GM12872	blood:	n/a	chr5:1801687-1801700
37	POLR2A	chr5:1798976-1802439	Hela-S3	cervix:	n/a	n/a
38	PML	chr5:1801218-1801825	K562	blood:	n/a	n/a
39	TAF1	chr5:1801090-1802017	ECC-1	luminal epithelium:	n/a	n/a
40	TAF7	chr5:1801343-1801837	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr5:1801680-1801830	HepG2	liver:	n/a	chr5:1801687-1801700
42	CCNT2	chr5:1801305-1801927	K562	blood:	n/a	chr5:1801422-1801431
43	TFAP2C	chr5:1799840-1802225	Hela-S3	cervix:	n/a	n/a
44	TCF3	chr5:1801372-1801869	GM12878	blood:	n/a	n/a
45	POLR2A	chr5:1800367-1801848	PFSK-1	brain:	n/a	n/a
46	HEY1	chr5:1801226-1801839	HepG2	liver:	n/a	chr5:1801758-1801773
47	YY1	chr5:1801096-1801948	GM12892	blood:	n/a	chr5:1801527-1801539 chr5:1801422-1801431
48	CTCF	chr5:1801436-1801708	T-47D	breast:	n/a	chr5:1801687-1801700
49	SMC3	chr5:1799868-1801925	Hela-S3	cervix:	n/a	chr5:1801716-1801723 chr5:1801424-1801434
50	TCF7L2	chr5:1801121-1801892	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:1799841..1802509-chr5:1881368..1882987,2	K562	blood:
2	chr12:53399938..53400804-chr5:1801437..1802026,2	Hela-S3	cervix:
3	chr5:1799569..1802884-chr5:1886598..1889173,4	MCF-7	breast:
4	chr16:2014889..2015472-chr5:1801226..1802047,2	Hela-S3	cervix:
5	chr19:1248358..1249071-chr5:1801127..1802076,2	Hela-S3	cervix:
6	chr15:57025323..57025921-chr5:1801018..1801848,2	Hela-S3	cervix:
7	chr17:73716503..73719364-chr5:1799934..1802626,2	MCF-7	breast:
8	chr12:120728613..120731132-chr5:1800155..1802952,2	MCF-7	breast:
9	chr1:87379579..87380541-chr5:1800717..1801693,2	Hela-S3	cervix:
10	chr5:1793765..1806799-chr5:1879445..1889322,45	MCF-7	breast:
11	chr5:891450..893942-chr5:1800895..1802661,2	K562	blood:
12	chr17:37792994..37793773-chr5:1801500..1802235,2	Hela-S3	cervix:
13	chr5:1344287..1345865-chr5:1799704..1802609,2	K562	blood:
14	chr5:1796457..1805482-chr5:1878036..1885786,21	MCF-7	breast:
15	chr5:1343974..1345787-chr5:1800029..1802609,2	K562	blood:
16	chr5:1801625..1804390-chr5:1831978..1833592,2	K562	blood:

Variant related genes	Relation type
MRPL36	TF binding region
ENSG00000249326	Chromatin interaction
ENSG00000183291	Chromatin interaction
ENSG00000153936	Chromatin interaction
ENSG00000131748	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000063046	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000249116	Chromatin interaction
ENSG00000132470	Chromatin interaction
ENSG00000113430	Chromatin interaction
ENSG00000137871	Chromatin interaction
ENSG00000028310	Chromatin interaction
ENSG00000049656	Chromatin interaction
ENSG00000255198	Chromatin interaction
ENSG00000071539	Chromatin interaction
ENSG00000167470	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11133910	0.89[ASN][1000 genomes]
rs11133911	0.86[ASN][1000 genomes]
rs11133912	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13187162	0.84[ASN][1000 genomes]
rs1845288	0.89[ASN][1000 genomes]
rs1873926	0.89[ASN][1000 genomes]
rs2276986	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2291944	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34233926	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35380881	0.86[ASN][1000 genomes]
rs3756343	0.87[ASN][1000 genomes]
rs3756345	0.91[ASN][1000 genomes]
rs3756346	0.91[ASN][1000 genomes]
rs3776141	0.90[ASN][1000 genomes]
rs3776142	0.91[ASN][1000 genomes]
rs3776143	0.91[ASN][1000 genomes]
rs3776144	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3776145	0.89[ASN][1000 genomes]
rs3776146	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3776149	0.89[ASN][1000 genomes]
rs3822364	0.91[ASN][1000 genomes]
rs4147769	0.89[ASN][1000 genomes]
rs4147770	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4147772	0.89[ASN][1000 genomes]
rs4147773	0.89[ASN][1000 genomes]
rs4975848	0.89[ASN][1000 genomes]
rs4975849	0.91[ASN][1000 genomes]
rs4975851	0.86[ASN][1000 genomes]
rs4975852	0.86[ASN][1000 genomes]
rs4975853	0.86[ASN][1000 genomes]
rs55883912	0.87[ASN][1000 genomes]
rs6555012	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6863367	0.87[ASN][1000 genomes]
rs7702843	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs972890	0.89[ASN][1000 genomes]
rs972891	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs972892	0.89[ASN][1000 genomes]
rs974722	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
3	nsv1034552	chr5:1658338-1856553	Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
4	nsv537606	chr5:1658338-1856553	Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
5	nsv1033147	chr5:1717303-1815821	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
6	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv1020703	chr5:1724199-1814288	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
8	nsv537608	chr5:1724199-1814288	Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
9	nsv1024133	chr5:1736691-1826510	Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers 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	40 gene(s)	inside rSNPs	diseases
10	nsv537609	chr5:1736691-1826510	Genic enhancers Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1798400-1802400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:1798800-1802200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr5:1798800-1802400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr5:1798800-1802800	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr5:1799000-1802200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:1799000-1802200	Active TSS	Left Ventricle	heart
7	chr5:1799000-1802400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:1799000-1802400	Active TSS	H9 Cell Line	embryonic stem cell
9	chr5:1799000-1802400	Active TSS	Psoas Muscle	Psoas
10	chr5:1799000-1802600	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr5:1799000-1802600	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr5:1799000-1802600	Active TSS	Fetal Intestine Small	intestine
13	chr5:1799000-1802600	Active TSS	A549	lung
14	chr5:1799200-1802200	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr5:1799200-1802200	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr5:1799200-1802200	Active TSS	Aorta	Aorta
17	chr5:1799200-1802200	Active TSS	Fetal Kidney	kidney
18	chr5:1799200-1802200	Active TSS	Sigmoid Colon	Sigmoid Colon
19	chr5:1799200-1802200	Active TSS	Small Intestine	intestine
20	chr5:1799200-1802200	Active TSS	NHDF-Ad	bronchial
21	chr5:1799200-1802400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr5:1799200-1802600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr5:1799200-1802600	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr5:1799200-1802800	Active TSS	GM12878-XiMat	blood
25	chr5:1799400-1801800	Active TSS	Fetal Brain Female	brain
26	chr5:1799400-1802000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr5:1799400-1802000	Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr5:1799400-1802000	Active TSS	Brain Anterior Caudate	brain
29	chr5:1799400-1802000	Active TSS	Brain Germinal Matrix	brain
30	chr5:1799400-1802000	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr5:1799400-1802000	Active TSS	Colon Smooth Muscle	Colon
32	chr5:1799400-1802000	Active TSS	Stomach Mucosa	stomach
33	chr5:1799400-1802000	Active TSS	Thymus	Thymus
34	chr5:1799400-1802000	Active TSS	Spleen	Spleen
35	chr5:1799400-1802000	Active TSS	Dnd41	blood
36	chr5:1799400-1802200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr5:1799400-1802200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:1799400-1802200	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr5:1799400-1802200	Active TSS	Brain Angular Gyrus	brain
40	chr5:1799400-1802200	Active TSS	Brain Hippocampus Middle	brain
41	chr5:1799400-1802200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr5:1799400-1802200	Active TSS	Brain Substantia Nigra	brain
43	chr5:1799400-1802200	Active TSS	Esophagus	oesophagus
44	chr5:1799400-1802200	Active TSS	Gastric	stomach
45	chr5:1799400-1802200	Active TSS	Ovary	ovary
46	chr5:1799400-1802400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr5:1799400-1802400	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr5:1799400-1802400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr5:1799400-1802400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr5:1799400-1802400	Active TSS	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links