Variant report

Variant	rs17026005
Chromosome Location	chr2:40661798-40661799
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	JUN	chr2:40661684-40662487	HUVEC	blood vessel:	n/a	chr2:40661917-40661928 chr2:40662176-40662184
2	JUND	chr2:40661606-40662775	SK-N-SH	brain:	n/a	chr2:40661917-40661928 chr2:40662176-40662184
3	TCF12	chr2:40661707-40662674	A549	lung:	n/a	n/a
4	NFIC	chr2:40661674-40662832	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr2:40660718-40662820	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr2:40661790-40662447	U87	brain:	n/a	n/a
7	SP1	chr2:40661778-40662552	HCT-116	colon:	n/a	n/a
8	GATA2	chr2:40661718-40662604	HUVEC	blood vessel:	n/a	n/a
9	TEAD4	chr2:40661726-40662733	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr2:40661738-40662432	HUVEC	blood vessel:	n/a	n/a
11	FOS	chr2:40661761-40662455	MCF10A-Er-Src	breast:	n/a	chr2:40661917-40661928 chr2:40662174-40662185 chr2:40662176-40662184
12	PBX3	chr2:40661734-40662696	SK-N-SH	brain:	n/a	chr2:40662252-40662261
13	GATA3	chr2:40661747-40662764	A549	lung:	n/a	n/a
14	TEAD4	chr2:40661698-40662592	SK-N-SH	brain:	n/a	n/a
15	EP300	chr2:40661696-40662730	SK-N-SH	brain:	n/a	chr2:40661829-40661837
16	EP300	chr2:40661659-40662736	SK-N-SH	brain:	n/a	chr2:40661829-40661837
17	POLR2A	chr2:40661790-40662441	U87	brain:	n/a	n/a
18	FOS	chr2:40661552-40662499	MCF10A-Er-Src	breast:	n/a	chr2:40661917-40661928 chr2:40662174-40662185 chr2:40662176-40662184
19	STAT3	chr2:40661732-40662521	Hela-S3	cervix:	n/a	chr2:40662026-40662037
20	JUND	chr2:40660723-40662766	SK-N-SH	brain:	n/a	chr2:40661917-40661928 chr2:40662176-40662184
21	EP300	chr2:40661478-40662548	Hela-S3	cervix:	n/a	chr2:40661829-40661837 chr2:40661482-40661496
22	CEBPB	chr2:40661776-40662656	Hela-S3	cervix:	n/a	n/a
23	TCF12	chr2:40661600-40662701	SK-N-SH	brain:	n/a	n/a
24	TBP	chr2:40661623-40662396	Hela-S3	cervix:	n/a	n/a
25	RCOR1	chr2:40661722-40662585	Hela-S3	cervix:	n/a	n/a
26	FOSL2	chr2:40661675-40662660	SK-N-SH	brain:	n/a	chr2:40661917-40661928 chr2:40662176-40662184
27	JUND	chr2:40661711-40662754	SK-N-SH	brain:	n/a	chr2:40661917-40661928 chr2:40662176-40662184
28	SMARCC1	chr2:40661672-40662932	Hela-S3	cervix:	n/a	chr2:40662175-40662184
29	MAX	chr2:40661761-40662812	A549	lung:	n/a	n/a
30	EP300	chr2:40661788-40662602	A549	lung:	n/a	chr2:40661829-40661837
31	FOSL2	chr2:40661777-40662663	A549	lung:	n/a	chr2:40661917-40661928 chr2:40662176-40662184
32	GATA3	chr2:40660758-40662717	SK-N-SH	brain:	n/a	chr2:40661679-40661688 chr2:40661681-40661688 chr2:40661679-40661689 chr2:40661674-40661695 chr2:40661681-40661688 chr2:40661676-40661692 chr2:40661681-40661688
33	GATA3	chr2:40660666-40662796	SK-N-SH	brain:	n/a	chr2:40661679-40661688 chr2:40661681-40661688 chr2:40662764-40662774 chr2:40661679-40661689 chr2:40661674-40661695 chr2:40661681-40661688 chr2:40661676-40661692 chr2:40661681-40661688
34	POLR2A	chr2:40661772-40662400	HUVEC	blood vessel:	n/a	n/a
35	JUN	chr2:40661730-40662558	Hela-S3	cervix:	n/a	chr2:40661917-40661928 chr2:40662176-40662184

Variant related genes	Relation type
SLC8A1	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10490043	0.85[CEU][hapmap]
rs12996425	1.00[CEU][hapmap]
rs12999886	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13031545	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13031785	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13031843	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13031849	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13035085	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17025926	0.85[CEU][hapmap]
rs17025999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17026001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17026003	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17026009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17026011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17026012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17026014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17026018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1990609	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs34038561	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34682370	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35321042	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35478019	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35797248	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35923316	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4993292	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs57193459	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61629255	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71439297	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71439298	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71439299	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7603114	0.89[CHB][hapmap];0.80[JPT][hapmap]

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	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2757794	chr2:40547947-40733776	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2759044	chr2:40547947-40733776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40646600-40670800	Weak transcription	Fetal Brain Female	brain
2	chr2:40647600-40662200	Weak transcription	Brain Germinal Matrix	brain
3	chr2:40648000-40667200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:40648200-40676400	Weak transcription	Fetal Kidney	kidney
5	chr2:40653000-40674800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:40654200-40662200	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:40655000-40665000	Weak transcription	Fetal Brain Male	brain
8	chr2:40657000-40671200	Weak transcription	Fetal Stomach	stomach
9	chr2:40657200-40662000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:40657800-40663000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:40657800-40666600	Enhancers	Colon Smooth Muscle	Colon
12	chr2:40658000-40663600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:40658000-40664000	Enhancers	NHDF-Ad	bronchial
14	chr2:40658000-40664200	Enhancers	HMEC	breast
15	chr2:40658200-40661800	Enhancers	HSMMtube	muscle
16	chr2:40658200-40662200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:40658200-40663400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:40658200-40663600	Enhancers	Osteobl	bone
19	chr2:40658200-40665400	Enhancers	NHLF	lung
20	chr2:40658400-40663600	Enhancers	Adipose Nuclei	Adipose
21	chr2:40658600-40661800	Enhancers	NHEK	skin
22	chr2:40658600-40663400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:40658600-40663800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:40658800-40662000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:40658800-40662800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:40659000-40662200	Weak transcription	Ovary	ovary
27	chr2:40659200-40662000	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr2:40659200-40662000	Weak transcription	Brain Anterior Caudate	brain
29	chr2:40659200-40663400	Enhancers	Hela-S3	cervix
30	chr2:40659600-40663200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:40659800-40662000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:40659800-40662000	Weak transcription	Right Atrium	heart
33	chr2:40659800-40664000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:40659800-40665600	Weak transcription	Dnd41	blood
35	chr2:40660000-40662000	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr2:40660000-40663200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr2:40660200-40663400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:40660200-40663400	Enhancers	HSMM	muscle
39	chr2:40660400-40661800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:40660600-40661800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr2:40660600-40663800	Enhancers	HUVEC	blood vessel
42	chr2:40660800-40662200	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr2:40660800-40663600	Enhancers	Aorta	Aorta
44	chr2:40660800-40664600	Enhancers	Left Ventricle	heart
45	chr2:40661000-40662000	Enhancers	NH-A	brain
46	chr2:40661000-40662200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:40661000-40664600	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr2:40661200-40661800	Weak transcription	Esophagus	oesophagus
49	chr2:40661200-40662000	Weak transcription	Fetal Muscle Leg	muscle
50	chr2:40661400-40661800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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