Variant report

Variant	rs879017
Chromosome Location	chr5:75842971-75842972
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	CHD1	chr5:75842578-75843813	GM12878	blood:	n/a	n/a
2	MTA3	chr5:75842104-75844288	GM12878	blood:	n/a	n/a
3	CHD2	chr5:75842229-75844299	GM12878	blood:	n/a	n/a
4	FOXA1	chr5:75842654-75843048	HepG2	liver:	n/a	n/a
5	POLR2A	chr5:75842198-75842994	GM12891	blood:	n/a	n/a
6	SP1	chr5:75842196-75842973	GM12878	blood:	n/a	n/a
7	ARID3A	chr5:75842649-75843062	HepG2	liver:	n/a	n/a
8	FOXM1	chr5:75842485-75843003	GM12878	blood:	n/a	n/a
9	BHLHE40	chr5:75842244-75843807	GM12878	blood:	n/a	n/a
10	HNF4G	chr5:75842736-75843018	HepG2	liver:	n/a	chr5:75842861-75842869 chr5:75842858-75842870 chr5:75842857-75842871 chr5:75842858-75842870
11	RELA	chr5:75842401-75843621	GM18505	blood:	n/a	n/a
12	BCLAF1	chr5:75842536-75843685	GM12878	blood:	n/a	chr5:75843310-75843319
13	TEAD4	chr5:75842635-75843180	HepG2	liver:	n/a	n/a
14	IRF3	chr5:75842957-75843503	GM12878	blood:	n/a	chr5:75843308-75843321 chr5:75843305-75843319 chr5:75843307-75843327 chr5:75843308-75843321 chr5:75843309-75843323 chr5:75843305-75843322 chr5:75843303-75843320 chr5:75843083-75843092 chr5:75843309-75843319 chr5:75843307-75843318 chr5:75843308-75843319
15	POLR2A	chr5:75842572-75843906	GM12878	blood:	n/a	n/a
16	MTA3	chr5:75842283-75843064	GM12878	blood:	n/a	n/a
17	IRF4	chr5:75842330-75842988	GM12878	blood:	n/a	n/a
18	RUNX3	chr5:75842112-75843749	GM12878	blood:	n/a	chr5:75843370-75843379 chr5:75843370-75843379
19	TBP	chr5:75842238-75843640	GM12878	blood:	n/a	n/a
20	CEBPB	chr5:75842800-75843138	HepG2	liver:	n/a	n/a
21	CREB1	chr5:75842171-75843766	GM12878	blood:	n/a	n/a
22	TBL1XR1	chr5:75842254-75843581	GM12878	blood:	n/a	n/a
23	POLR2A	chr5:75842276-75843059	GM12892	blood:	n/a	n/a
24	PML	chr5:75842413-75843762	GM12878	blood:	n/a	n/a
25	NFIC	chr5:75842272-75843807	GM12878	blood:	n/a	n/a
26	MXI1	chr5:75842230-75843966	GM12878	blood:	n/a	n/a
27	MAX	chr5:75842383-75843905	GM12878	blood:	n/a	n/a
28	POLR2A	chr5:75842274-75843535	GM12878	blood:	n/a	n/a
29	PAX5	chr5:75842107-75843023	GM12878	blood:	n/a	chr5:75842697-75842706 chr5:75842793-75842803 chr5:75842758-75842767 chr5:75842431-75842440 chr5:75842444-75842453
30	FOXA1	chr5:75842559-75843079	HepG2	liver:	n/a	n/a
31	NRF1	chr5:75842886-75843600	GM12878	blood:	n/a	n/a
32	ATF2	chr5:75842225-75843735	GM12878	blood:	n/a	n/a
33	RCOR1	chr5:75842337-75843982	GM12878	blood:	n/a	n/a
34	MAZ	chr5:75842632-75843695	GM12878	blood:	n/a	n/a
35	EP300	chr5:75842174-75843737	GM12878	blood:	n/a	chr5:75842431-75842445
36	POLR2A	chr5:75842228-75843863	GM12878	blood:	n/a	n/a
37	CREB1	chr5:75842110-75843015	GM12878	blood:	n/a	n/a
38	EP300	chr5:75842171-75843681	GM12878	blood:	n/a	chr5:75842431-75842445
39	POLR2A	chr5:75842273-75843040	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
IQGAP2	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10462543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11948805	0.86[JPT][hapmap]
rs12513400	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12513594	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12513678	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12519094	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12519329	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12519473	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12521026	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12523647	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1501788	0.95[JPT][hapmap]
rs1566	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17680732	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17680756	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17680811	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17748322	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2270908	0.82[AMR][1000 genomes]
rs3736394	0.95[JPT][hapmap]
rs3756514	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3797388	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap]
rs3912001	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4703713	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4704329	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4704340	0.83[ASN][1000 genomes]
rs55699952	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56338424	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58087114	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60881227	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61014011	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61233297	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs869733	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs873787	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022032	chr5:75785106-75914003	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer 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	3 gene(s)	inside rSNPs	diseases
2	nsv598679	chr5:75823965-75914729	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1023953	chr5:75831037-75913784	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1026257	chr5:75831037-75914003	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1016823	chr5:75831037-75915905	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv598680	chr5:75839165-75914729	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS 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	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75835600-75871200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:75839600-75845400	Enhancers	HepG2	liver
3	chr5:75839600-75845800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:75839600-75846000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr5:75840200-75843200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr5:75840400-75843000	Weak transcription	Fetal Intestine Large	intestine
7	chr5:75840400-75843600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr5:75840600-75843000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr5:75841000-75843200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
10	chr5:75841200-75843000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr5:75841800-75843000	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr5:75841800-75843000	Enhancers	Primary B cells from cord blood	blood
13	chr5:75842000-75843000	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr5:75842000-75843800	Enhancers	Fetal Muscle Leg	muscle
15	chr5:75842000-75844600	Enhancers	Primary B cells from peripheral blood	blood
16	chr5:75842000-75845800	Enhancers	Stomach Mucosa	stomach
17	chr5:75842200-75843400	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr5:75842200-75843400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:75842200-75843600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:75842200-75843600	Enhancers	Pancreas	Pancrea
21	chr5:75842200-75843800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr5:75842200-75844200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr5:75842200-75844400	Enhancers	Fetal Thymus	thymus
24	chr5:75842200-75844600	Flanking Active TSS	GM12878-XiMat	blood
25	chr5:75842200-75844800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr5:75842200-75845800	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr5:75842400-75843000	Enhancers	Brain Anterior Caudate	brain
28	chr5:75842400-75843000	Enhancers	Lung	lung
29	chr5:75842400-75843000	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr5:75842400-75843200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr5:75842400-75843200	Enhancers	Adipose Nuclei	Adipose
32	chr5:75842400-75843200	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr5:75842400-75843200	Enhancers	Right Atrium	heart
34	chr5:75842400-75843400	Enhancers	Fetal Brain Male	brain
35	chr5:75842400-75843600	Enhancers	K562	blood
36	chr5:75842400-75843800	Enhancers	H9 Cell Line	embryonic stem cell
37	chr5:75842400-75843800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr5:75842400-75843800	Enhancers	Fetal Kidney	kidney
39	chr5:75842400-75844000	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr5:75842400-75844000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr5:75842400-75844200	Enhancers	Fetal Stomach	stomach
42	chr5:75842400-75844400	Enhancers	Placenta	Placenta
43	chr5:75842400-75844800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr5:75842400-75844800	Enhancers	Small Intestine	intestine
45	chr5:75842400-75845000	Enhancers	Fetal Intestine Small	intestine
46	chr5:75842400-75845600	Enhancers	Gastric	stomach
47	chr5:75842600-75843000	Enhancers	Brain Substantia Nigra	brain
48	chr5:75842600-75843000	Enhancers	Thymus	Thymus
49	chr5:75842600-75843200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr5:75842600-75843400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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