Variant report

Variant	rs2659539
Chromosome Location	chr4:102121344-102121345
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	chr4:102121087-102121373	HCT-116	colon:	n/a	n/a
2	FOS	chr4:102121138-102122207	MCF10A-Er-Src	breast:	n/a	chr4:102121301-102121311 chr4:102121301-102121311 chr4:102121301-102121311 chr4:102121302-102121310 chr4:102121972-102121983
3	FOSL2	chr4:102121000-102121555	SK-N-SH	brain:	n/a	chr4:102121301-102121311 chr4:102121301-102121311 chr4:102121301-102121311 chr4:102121302-102121310
4	FOS	chr4:102121214-102121525	MCF10A-Er-Src	breast:	n/a	chr4:102121301-102121311 chr4:102121301-102121311 chr4:102121301-102121311 chr4:102121302-102121310
5	PBX3	chr4:102121075-102121548	SK-N-SH	brain:	n/a	n/a
6	GATA2	chr4:102121300-102122097	HUVEC	blood vessel:	n/a	n/a
7	RAD21	chr4:102121048-102121425	SK-N-SH_RA	brain:	n/a	n/a
8	POLR2A	chr4:102121087-102121459	SK-N-SH	brain:	n/a	n/a
9	NFIC	chr4:102120984-102121649	SK-N-SH	brain:	n/a	n/a
10	TCF12	chr4:102120941-102122333	SK-N-SH	brain:	n/a	n/a
11	GATA3	chr4:102120893-102122261	SK-N-SH	brain:	n/a	chr4:102120974-102120981
12	EP300	chr4:102121085-102121452	SK-N-SH_RA	brain:	n/a	n/a
13	STAT3	chr4:102121206-102121406	MCF10A-Er-Src	breast:	n/a	n/a
14	GATA3	chr4:102121003-102121711	SK-N-SH	brain:	n/a	n/a
15	TCF12	chr4:102120845-102122208	SK-N-SH	brain:	n/a	n/a
16	JUND	chr4:102121015-102122310	SK-N-SH	brain:	n/a	chr4:102121301-102121311 chr4:102121301-102121311 chr4:102121301-102121311 chr4:102121302-102121310 chr4:102121994-102122005 chr4:102121972-102121983

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:102112038..102115219-chr4:102118263..102121528,3	MCF-7	breast:

Variant related genes	Relation type
PPP3CA	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1021965	0.85[ASN][1000 genomes]
rs1354785	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395475	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395476	0.85[ASN][1000 genomes]
rs1506799	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1506800	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1506802	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1506803	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1506804	0.85[ASN][1000 genomes]
rs1543856	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17030851	0.81[ASN][1000 genomes]
rs2135610	0.85[ASN][1000 genomes]
rs2135614	0.80[ASN][1000 genomes]
rs2174683	0.80[ASN][1000 genomes]
rs2659503	0.85[ASN][1000 genomes]
rs2659504	0.85[ASN][1000 genomes]
rs2659505	0.85[ASN][1000 genomes]
rs2659506	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2659508	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2659509	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659511	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659512	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659513	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659532	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2659533	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659534	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659537	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659538	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659541	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659542	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2850980	0.85[ASN][1000 genomes]
rs2850981	0.85[ASN][1000 genomes]
rs2850982	0.85[ASN][1000 genomes]
rs2850985	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850987	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850989	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850990	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2850991	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850994	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850995	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3804366	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4478191	0.82[ASN][1000 genomes]
rs73833252	0.83[ASN][1000 genomes]
rs931871	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers 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 miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102105400-102126200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr4:102106200-102121600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:102107600-102126600	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr4:102109200-102126200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr4:102109800-102122600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr4:102111200-102122400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:102113200-102122400	Weak transcription	Aorta	Aorta
8	chr4:102113200-102124400	Weak transcription	Pancreas	Pancrea
9	chr4:102113600-102121400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:102113600-102122800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr4:102113800-102122800	Weak transcription	Right Atrium	heart
12	chr4:102113800-102126200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr4:102113800-102127200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr4:102113800-102131800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr4:102117000-102121600	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr4:102117200-102125800	Weak transcription	Dnd41	blood
17	chr4:102117200-102126200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr4:102117600-102121400	Enhancers	Fetal Intestine Small	intestine
19	chr4:102117600-102123000	Enhancers	HepG2	liver
20	chr4:102117800-102121800	Enhancers	Liver	Liver
21	chr4:102117800-102124200	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr4:102118000-102132600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr4:102118200-102121800	Enhancers	Colon Smooth Muscle	Colon
24	chr4:102118200-102126800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr4:102118800-102126200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr4:102119200-102121600	Enhancers	Fetal Intestine Large	intestine
27	chr4:102119200-102122200	Enhancers	Brain Anterior Caudate	brain
28	chr4:102119400-102121400	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr4:102119400-102121800	Enhancers	Primary B cells from cord blood	blood
30	chr4:102119400-102122800	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr4:102119400-102123200	Enhancers	Primary B cells from peripheral blood	blood
32	chr4:102119400-102123200	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr4:102119400-102123200	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr4:102119400-102123200	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr4:102119600-102121600	Enhancers	Brain Hippocampus Middle	brain
36	chr4:102119600-102121600	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr4:102119600-102121800	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr4:102119600-102121800	Enhancers	Fetal Brain Female	brain
39	chr4:102119600-102122000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr4:102119600-102122600	Enhancers	Brain Angular Gyrus	brain
41	chr4:102119600-102126200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr4:102119800-102121600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr4:102119800-102121600	Enhancers	Fetal Brain Male	brain
44	chr4:102119800-102121800	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr4:102119800-102121800	Flanking Active TSS	A549	lung
46	chr4:102120000-102121600	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr4:102120000-102122800	Enhancers	Duodenum Mucosa	Duodenum
48	chr4:102120000-102131400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr4:102120200-102121600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr4:102120200-102122800	Weak transcription	Gastric	stomach

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