Variant report

Variant	rs17026009
Chromosome Location	chr2:40662125-40662126
allele	G/T
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	chr2:40661853-40662588	HCT-116	colon:	n/a	chr2:40661917-40661928 chr2:40662176-40662184
2	SP1	chr2:40661902-40662552	HCT-116	colon:	n/a	n/a
3	JUN	chr2:40661684-40662487	HUVEC	blood vessel:	n/a	chr2:40661917-40661928 chr2:40662176-40662184
4	MYC	chr2:40662088-40662234	HUVEC	blood vessel:	n/a	n/a
5	JUND	chr2:40661606-40662775	SK-N-SH	brain:	n/a	chr2:40661917-40661928 chr2:40662176-40662184
6	TCF12	chr2:40661707-40662674	A549	lung:	n/a	n/a
7	REST	chr2:40662007-40662385	SK-N-SH	brain:	n/a	n/a
8	MAX	chr2:40661939-40662494	Hela-S3	cervix:	n/a	n/a
9	NFIC	chr2:40661873-40662547	SK-N-SH	brain:	n/a	n/a
10	STAT3	chr2:40662066-40662455	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr2:40661831-40662424	MCF10A-Er-Src	breast:	n/a	chr2:40661917-40661928 chr2:40662174-40662185 chr2:40662176-40662184
12	NFIC	chr2:40661674-40662832	SK-N-SH	brain:	n/a	n/a
13	TCF12	chr2:40660718-40662820	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr2:40661790-40662447	U87	brain:	n/a	n/a
15	USF1	chr2:40661935-40662472	A549	lung:	n/a	n/a
16	SP1	chr2:40661778-40662552	HCT-116	colon:	n/a	n/a
17	GATA2	chr2:40661718-40662604	HUVEC	blood vessel:	n/a	n/a
18	MAFK	chr2:40662110-40662499	IMR90	lung:	n/a	chr2:40662325-40662341
19	TEAD4	chr2:40661726-40662733	SK-N-SH	brain:	n/a	n/a
20	JUND	chr2:40662055-40662474	A549	lung:	n/a	chr2:40662176-40662184
21	POLR2A	chr2:40661738-40662432	HUVEC	blood vessel:	n/a	n/a
22	JUND	chr2:40661813-40662472	Hela-S3	cervix:	n/a	chr2:40661917-40661928 chr2:40662176-40662184
23	FOS	chr2:40661761-40662455	MCF10A-Er-Src	breast:	n/a	chr2:40661917-40661928 chr2:40662174-40662185 chr2:40662176-40662184
24	POLR2A	chr2:40661821-40662547	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr2:40662121-40662273	MCF10A-Er-Src	breast:	n/a	n/a
26	PBX3	chr2:40661734-40662696	SK-N-SH	brain:	n/a	chr2:40662252-40662261
27	CTCF	chr2:40662040-40662190	AG04449	skin:	n/a	n/a
28	GATA3	chr2:40661747-40662764	A549	lung:	n/a	n/a
29	TEAD4	chr2:40661698-40662592	SK-N-SH	brain:	n/a	n/a
30	PBX3	chr2:40661894-40662538	A549	lung:	n/a	chr2:40662252-40662261
31	SIN3AK20	chr2:40661881-40662557	SK-N-SH	brain:	n/a	n/a
32	USF2	chr2:40661983-40662385	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr2:40662015-40662477	HUVEC	blood vessel:	n/a	n/a
34	FOS	chr2:40661955-40662422	MCF10A-Er-Src	breast:	n/a	chr2:40662174-40662185 chr2:40662176-40662184
35	YY1	chr2:40661990-40662391	SK-N-SH_RA	brain:	n/a	n/a
36	JUND	chr2:40661904-40662487	A549	lung:	n/a	chr2:40661917-40661928 chr2:40662176-40662184
37	FOSL2	chr2:40661862-40662516	SK-N-SH	brain:	n/a	chr2:40661917-40661928 chr2:40662176-40662184
38	FOSL1	chr2:40661820-40662539	HCT-116	colon:	n/a	chr2:40661917-40661928 chr2:40662176-40662184
39	EP300	chr2:40661696-40662730	SK-N-SH	brain:	n/a	chr2:40661829-40661837
40	POLR2A	chr2:40661885-40662368	HUVEC	blood vessel:	n/a	n/a
41	EP300	chr2:40661659-40662736	SK-N-SH	brain:	n/a	chr2:40661829-40661837
42	TEAD4	chr2:40661808-40662631	A549	lung:	n/a	n/a
43	POLR2A	chr2:40661790-40662441	U87	brain:	n/a	n/a
44	FOS	chr2:40661552-40662499	MCF10A-Er-Src	breast:	n/a	chr2:40661917-40661928 chr2:40662174-40662185 chr2:40662176-40662184
45	SP1	chr2:40661845-40662601	A549	lung:	n/a	n/a
46	JUND	chr2:40661815-40662603	HCT-116	colon:	n/a	chr2:40661917-40661928 chr2:40662176-40662184
47	TEAD4	chr2:40661896-40662520	HCT-116	colon:	n/a	n/a
48	STAT3	chr2:40661732-40662521	Hela-S3	cervix:	n/a	chr2:40662026-40662037
49	JUND	chr2:40660723-40662766	SK-N-SH	brain:	n/a	chr2:40661917-40661928 chr2:40662176-40662184
50	TFAP2C	chr2:40661972-40662807	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:40662045..40663958-chr2:40665740..40668580,2	MCF-7	breast:

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];0.83[ASN][1000 genomes]
rs13031545	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13031785	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13031843	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13031849	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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];0.92[ASN][1000 genomes]
rs17025926	0.85[CEU][hapmap]
rs17025999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[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];0.96[ASN][1000 genomes]
rs17026003	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17026005	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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17026012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17026014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17026018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1990609	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs34038561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34682370	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35321042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35478019	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35797248	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35923316	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4993292	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs57193459	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61629255	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71439297	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71439298	1.00[AFR][1000 genomes];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	0.90[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:63 , 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	chr2:40657800-40663000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:40657800-40666600	Enhancers	Colon Smooth Muscle	Colon
11	chr2:40658000-40663600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:40658000-40664000	Enhancers	NHDF-Ad	bronchial
13	chr2:40658000-40664200	Enhancers	HMEC	breast
14	chr2:40658200-40662200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:40658200-40663400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:40658200-40663600	Enhancers	Osteobl	bone
17	chr2:40658200-40665400	Enhancers	NHLF	lung
18	chr2:40658400-40663600	Enhancers	Adipose Nuclei	Adipose
19	chr2:40658600-40663400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:40658600-40663800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:40658800-40662800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:40659000-40662200	Weak transcription	Ovary	ovary
23	chr2:40659200-40663400	Enhancers	Hela-S3	cervix
24	chr2:40659600-40663200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:40659800-40664000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr2:40659800-40665600	Weak transcription	Dnd41	blood
27	chr2:40660000-40663200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr2:40660200-40663400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:40660200-40663400	Enhancers	HSMM	muscle
30	chr2:40660600-40663800	Enhancers	HUVEC	blood vessel
31	chr2:40660800-40662200	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr2:40660800-40663600	Enhancers	Aorta	Aorta
33	chr2:40660800-40664600	Enhancers	Left Ventricle	heart
34	chr2:40661000-40662200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:40661000-40664600	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr2:40661400-40662400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr2:40661600-40662200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:40661600-40662800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr2:40661600-40662800	Flanking Active TSS	A549	lung
40	chr2:40661600-40663000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:40661600-40663600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:40661800-40662200	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr2:40661800-40662200	Flanking Active TSS	NHEK	skin
44	chr2:40661800-40662400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:40661800-40662400	Enhancers	Esophagus	oesophagus
46	chr2:40661800-40662400	Enhancers	Right Ventricle	heart
47	chr2:40661800-40662800	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr2:40661800-40662800	Enhancers	Placenta Amnion	Placenta Amnion
49	chr2:40661800-40662800	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr2:40661800-40663400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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