Variant report

Variant	rs34470469
Chromosome Location	chr3:98499528-98499529
allele	C/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	GATA2	chr3:98498824-98499746	HUVEC	blood vessel:	n/a	chr3:98499048-98499057 chr3:98499048-98499057 chr3:98499225-98499241 chr3:98499313-98499323 chr3:98499043-98499057
2	POLR2A	chr3:98498725-98499756	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr3:98499347-98499843	U87	brain:	n/a	n/a
4	FOS	chr3:98498632-98499544	HUVEC	blood vessel:	n/a	chr3:98498966-98498977
5	JUN	chr3:98498760-98499582	HUVEC	blood vessel:	n/a	chr3:98499569-98499580
6	POLR2A	chr3:98499303-98499843	U87	brain:	n/a	n/a
7	GATA3	chr3:98498508-98499601	SK-N-SH	brain:	n/a	chr3:98499048-98499057 chr3:98499048-98499057 chr3:98499225-98499241 chr3:98499313-98499323
8	POLR2A	chr3:98498651-98499815	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
ST3GAL6	TF binding region
PDLIM1P4	TF binding region

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10428160	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10589669	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11552978	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12107272	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12108018	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12108142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13059624	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13065136	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13068317	1.00[AMR][1000 genomes]
rs13072410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13074614	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13074787	0.82[AMR][1000 genomes]
rs13076960	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13080057	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13081992	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13083238	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13083613	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13083934	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13084692	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13087627	0.85[EUR][1000 genomes]
rs13087631	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13088532	0.91[AMR][1000 genomes]
rs13091170	0.81[EUR][1000 genomes]
rs13091236	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13093128	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13096085	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13097876	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13100915	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13100937	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34008360	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34269725	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34279227	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34284740	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34394867	1.00[AMR][1000 genomes]
rs34489202	0.85[EUR][1000 genomes]
rs34688367	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34711372	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34725039	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34826460	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34848749	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34860591	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34951301	0.85[EUR][1000 genomes]
rs35006699	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35025156	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35076733	0.81[EUR][1000 genomes]
rs35098355	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35103318	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35219252	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35234681	1.00[AMR][1000 genomes]
rs35239055	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35312318	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35366262	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35422064	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35499232	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35514544	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35526367	1.00[AMR][1000 genomes]
rs35539438	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35764973	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35914268	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35947806	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs36032715	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36098932	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36157152	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36175276	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41267851	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55644421	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56083233	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56094988	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56246599	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6764579	1.00[AMR][1000 genomes]
rs6805362	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71311393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71311394	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71311397	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71311398	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71311402	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71313504	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71313508	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71313509	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71313510	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71313511	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7614053	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98478800-98515200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr3:98482600-98501800	Weak transcription	Fetal Stomach	stomach
3	chr3:98483000-98517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:98483200-98518000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:98483600-98513600	Weak transcription	Brain Germinal Matrix	brain
6	chr3:98483800-98515000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:98484000-98514000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:98484200-98515200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
10	chr3:98489800-98503000	Weak transcription	Psoas Muscle	Psoas
11	chr3:98490200-98525200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:98492200-98517800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:98493800-98499600	Enhancers	Fetal Intestine Large	intestine
14	chr3:98494600-98506000	Enhancers	Aorta	Aorta
15	chr3:98495800-98499600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr3:98496000-98499600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:98496000-98499600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:98496000-98499800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:98496000-98499800	Enhancers	NH-A	brain
20	chr3:98496200-98499600	Enhancers	Brain Cingulate Gyrus	brain
21	chr3:98496200-98499800	Enhancers	Brain Substantia Nigra	brain
22	chr3:98496400-98499800	Enhancers	Brain Anterior Caudate	brain
23	chr3:98496600-98499600	Enhancers	Adipose Nuclei	Adipose
24	chr3:98496600-98503800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:98496800-98502800	Weak transcription	Fetal Thymus	thymus
26	chr3:98497000-98524600	Weak transcription	Fetal Brain Male	brain
27	chr3:98497400-98499600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:98497400-98499800	Strong transcription	Dnd41	blood
29	chr3:98497400-98501800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:98497400-98503600	Enhancers	Placenta	Placenta
31	chr3:98497600-98499800	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr3:98497600-98502400	Weak transcription	Lung	lung
33	chr3:98497800-98517200	Weak transcription	Fetal Brain Female	brain
34	chr3:98498000-98499600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:98498000-98499600	Enhancers	Muscle Satellite Cultured Cells	--
36	chr3:98498000-98499800	Enhancers	HMEC	breast
37	chr3:98498000-98500400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:98498000-98500400	Weak transcription	Pancreas	Pancrea
39	chr3:98498000-98501800	Weak transcription	Gastric	stomach
40	chr3:98498000-98503000	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr3:98498000-98516600	Weak transcription	Stomach Mucosa	stomach
42	chr3:98498200-98499600	Enhancers	Brain Angular Gyrus	brain
43	chr3:98498200-98505400	Strong transcription	Thymus	Thymus
44	chr3:98498400-98499800	Genic enhancers	HepG2	liver
45	chr3:98498400-98500000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:98498400-98501600	Weak transcription	GM12878-XiMat	blood
47	chr3:98498400-98504600	Weak transcription	Fetal Intestine Small	intestine
48	chr3:98498600-98499600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:98498600-98499800	Strong transcription	Primary hematopoietic stem cells	blood
50	chr3:98498600-98499800	Enhancers	Osteobl	bone

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