Variant report

Variant	rs1374937
Chromosome Location	chr4:87860740-87860741
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	POLR2A	chr4:87860692-87861639	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:87860654-87861474	GM12892	blood:	n/a	n/a
3	POLR2A	chr4:87860676-87861349	GM12892	blood:	n/a	n/a
4	CHD1	chr4:87860148-87861127	GM12878	blood:	n/a	n/a
5	FOXA2	chr4:87860564-87860809	HepG2	liver:	n/a	n/a
6	EP300	chr4:87860737-87861509	GM12878	blood:	n/a	n/a
7	JUND	chr4:87860598-87860798	K562	blood:	n/a	n/a
8	RELA	chr4:87860392-87861533	GM12878	blood:	n/a	n/a
9	MXI1	chr4:87860267-87861248	GM12878	blood:	n/a	chr4:87860671-87860680
10	POLR2A	chr4:87860656-87861476	GM18505	blood:	n/a	n/a
11	MAZ	chr4:87860399-87861299	GM12878	blood:	n/a	chr4:87860671-87860681 chr4:87860671-87860682 chr4:87860672-87860681
12	FOXM1	chr4:87860630-87861547	GM12878	blood:	n/a	n/a
13	BCLAF1	chr4:87860616-87861590	GM12878	blood:	n/a	n/a
14	PML	chr4:87860666-87861616	GM12878	blood:	n/a	n/a
15	MEF2A	chr4:87860617-87861386	GM12878	blood:	n/a	chr4:87860708-87860729
16	FOXA1	chr4:87860183-87860812	HepG2	liver:	n/a	n/a
17	POU2F2	chr4:87860736-87861386	GM12878	blood:	n/a	n/a
18	MTA3	chr4:87860076-87862059	GM12878	blood:	n/a	n/a
19	TCF3	chr4:87860732-87861292	GM12878	blood:	n/a	n/a
20	STAT5A	chr4:87860642-87861587	GM12878	blood:	n/a	n/a
21	FOXM1	chr4:87860585-87861687	GM12878	blood:	n/a	n/a
22	IKZF1	chr4:87860734-87861570	GM12878	blood:	n/a	n/a
23	RCOR1	chr4:87860339-87861406	GM12878	blood:	n/a	n/a
24	MYC	chr4:87860348-87860834	K562	blood:	n/a	chr4:87860671-87860681 chr4:87860671-87860682 chr4:87860672-87860681
25	ELF1	chr4:87860733-87861266	GM12878	blood:	n/a	n/a
26	RUNX3	chr4:87860716-87861570	GM12878	blood:	n/a	n/a
27	CUX1	chr4:87860657-87861375	GM12878	blood:	n/a	n/a
28	RELA	chr4:87860739-87861717	GM15510	blood:	n/a	n/a
29	POLR2A	chr4:87859852-87861095	MCF10A-Er-Src	breast:	n/a	n/a
30	RELA	chr4:87860731-87861585	GM10847	blood:	n/a	n/a
31	NFIC	chr4:87860132-87861460	GM12878	blood:	n/a	n/a
32	SPI1	chr4:87860288-87860756	HL-60	blood:	n/a	n/a
33	POLR2A	chr4:87860698-87861793	GM12878	blood:	n/a	n/a
34	NFATC1	chr4:87860474-87861730	GM12878	blood:	n/a	n/a
35	NFATC1	chr4:87860712-87861681	GM12878	blood:	n/a	n/a
36	EBF1	chr4:87860317-87861252	GM12878	blood:	n/a	n/a
37	PML	chr4:87860738-87861155	GM12878	blood:	n/a	n/a
38	MEF2C	chr4:87860708-87861358	GM12878	blood:	n/a	chr4:87860708-87860729 chr4:87861033-87861048
39	MAX	chr4:87860301-87861372	GM12878	blood:	n/a	chr4:87860671-87860681 chr4:87860671-87860682 chr4:87860672-87860681
40	TBP	chr4:87860422-87861265	GM12878	blood:	n/a	n/a
41	NFIC	chr4:87860470-87861608	GM12878	blood:	n/a	n/a
42	BCLAF1	chr4:87860682-87861355	GM12878	blood:	n/a	n/a
43	MTA3	chr4:87860233-87861554	GM12878	blood:	n/a	n/a
44	ATF2	chr4:87860207-87861524	GM12878	blood:	n/a	n/a
45	SMC3	chr4:87860723-87861491	GM12878	blood:	n/a	n/a
46	ATF2	chr4:87860520-87861503	GM12878	blood:	n/a	n/a
47	BCL3	chr4:87860738-87861678	GM12878	blood:	n/a	n/a
48	TBL1XR1	chr4:87860310-87861367	GM12878	blood:	n/a	n/a
49	RUNX3	chr4:87860309-87861649	GM12878	blood:	n/a	n/a
50	RELA	chr4:87860316-87861552	GM18505	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:87859835..87862279-chr4:87865985..87868737,2	MCF-7	breast:
2	chr4:87860517..87862879-chr4:87877524..87879606,2	K562	blood:
3	chr4:87845889..87863516-chr4:87925389..87935181,79	K562	blood:
4	chr4:87853595..87871697-chr4:87924007..87941983,77	K562	blood:
5	chr4:87860293..87862516-chr4:87877340..87879546,2	MCF-7	breast:
6	chr4:87853395..87861870-chr4:87925425..87930611,18	MCF-7	breast:

Variant related genes	Relation type
C4orf36	TF binding region
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10003332	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs10008600	0.86[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs10022960	0.91[ASN][1000 genomes]
rs13119324	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1374936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1584345	0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs168161	0.83[ASN][1000 genomes]
rs17012291	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs1868245	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1972969	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs2053772	0.84[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2053774	0.92[ASN][1000 genomes]
rs2272777	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs2594276	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs2705617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs340627	0.80[ASN][1000 genomes]
rs340628	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs340629	0.80[ASN][1000 genomes]
rs340631	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs340635	0.83[ASN][1000 genomes]
rs340640	0.80[ASN][1000 genomes]
rs340644	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs340645	0.80[ASN][1000 genomes]
rs340647	0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs340649	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs340652	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs4536897	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs4693155	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs4693797	0.86[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4693799	0.86[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs6531943	0.85[ASN][1000 genomes]
rs6531944	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs6531945	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs6531947	0.80[ASN][1000 genomes]
rs6815546	0.86[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs6853011	0.91[ASN][1000 genomes]
rs73837575	0.80[ASN][1000 genomes]
rs7685248	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs895740	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs965824	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][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	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1013308	chr4:87769694-87870168	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv508297	chr4:87778783-87868508	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87856600-87861600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr4:87856800-87861400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr4:87857400-87860800	Weak transcription	Aorta	Aorta
4	chr4:87857400-87860800	Active TSS	Placenta	Placenta
5	chr4:87857400-87861600	Flanking Active TSS	Dnd41	blood
6	chr4:87857600-87882000	Weak transcription	Spleen	Spleen
7	chr4:87857800-87860800	Weak transcription	Esophagus	oesophagus
8	chr4:87857800-87860800	Weak transcription	Gastric	stomach
9	chr4:87857800-87861000	Weak transcription	Left Ventricle	heart
10	chr4:87857800-87861400	Weak transcription	Brain Angular Gyrus	brain
11	chr4:87857800-87867800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:87857800-87880200	Weak transcription	HSMM	muscle
13	chr4:87858000-87860800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr4:87858000-87861000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:87858000-87861000	Weak transcription	NH-A	brain
16	chr4:87858000-87867600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr4:87858200-87860800	Weak transcription	Brain Substantia Nigra	brain
18	chr4:87858200-87861000	Enhancers	Primary B cells from peripheral blood	blood
19	chr4:87858200-87861600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr4:87858200-87861600	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr4:87858200-87862000	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr4:87858200-87866800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr4:87858200-87869400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr4:87858400-87860800	Weak transcription	NHLF	lung
25	chr4:87858400-87861400	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr4:87858600-87861400	Enhancers	Rectal Smooth Muscle	rectum
27	chr4:87858600-87862000	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr4:87858600-87862400	Enhancers	Primary T cells fromperipheralblood	blood
29	chr4:87858600-87862400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr4:87858600-87863200	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr4:87858600-87864800	Enhancers	Fetal Thymus	thymus
32	chr4:87858600-87881000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr4:87858800-87860800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr4:87858800-87861000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr4:87858800-87864400	Enhancers	Liver	Liver
36	chr4:87859000-87861400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr4:87859000-87861600	Enhancers	Colon Smooth Muscle	Colon
38	chr4:87859000-87862200	Enhancers	Fetal Intestine Small	intestine
39	chr4:87859000-87864400	Enhancers	Fetal Intestine Large	intestine
40	chr4:87859200-87861400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:87859200-87865600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr4:87859400-87861400	Enhancers	H1 Cell Line	embryonic stem cell
43	chr4:87859400-87861600	Enhancers	Small Intestine	intestine
44	chr4:87859600-87860800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr4:87859600-87860800	Weak transcription	Lung	lung
46	chr4:87859600-87860800	Weak transcription	Psoas Muscle	Psoas
47	chr4:87859600-87861800	Enhancers	NHEK	skin
48	chr4:87859800-87860800	Flanking Active TSS	GM12878-XiMat	blood
49	chr4:87859800-87861000	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr4:87859800-87861000	Flanking Active TSS	Primary hematopoietic stem cells	blood

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