Variant report

Variant	rs3755569
Chromosome Location	chr3:98449742-98449743
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	NFATC1	chr3:98449130-98449750	GM12878	blood:	n/a	n/a
2	STAT5A	chr3:98449136-98449759	GM12878	blood:	n/a	n/a
3	MXI1	chr3:98449136-98449805	GM12878	blood:	n/a	chr3:98449298-98449307
4	POLR2A	chr3:98449108-98449809	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:98449139-98449824	GM12891	blood:	n/a	n/a
6	STAT1	chr3:98449195-98449798	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:98449043-98449870	GM12892	blood:	n/a	n/a
8	EBF1	chr3:98449140-98449742	GM12878	blood:	n/a	n/a
9	WRNIP1	chr3:98449217-98449791	GM12878	blood:	n/a	n/a
10	RUNX3	chr3:98449029-98449811	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:98449179-98449744	GM12892	blood:	n/a	n/a
12	RUNX3	chr3:98449156-98449800	GM12878	blood:	n/a	n/a
13	NFIC	chr3:98448914-98450026	GM12878	blood:	n/a	n/a
14	PML	chr3:98448957-98450209	GM12878	blood:	n/a	n/a
15	POLR2A	chr3:98449091-98449761	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
ST3GAL6	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10470451	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs115931	0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs11923134	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496694	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13315676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1440149	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1440155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1440158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1530655	0.87[CEU][hapmap];0.91[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1868217	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs278373	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs278374	0.82[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs28553326	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28707457	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3755570	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3772091	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3821358	0.87[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4638909	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56976804	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60464352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276459	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62278471	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62278472	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7611040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7614161	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7620634	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7620636	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7628381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7630887	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7631062	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7643537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7649812	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7652790	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs828593	0.91[ASN][1000 genomes]
rs828594	0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs828595	0.82[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs828596	0.82[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs828597	0.81[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs828598	0.82[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap]
rs828599	0.87[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs828602	0.86[ASN][1000 genomes]
rs828613	0.84[ASN][1000 genomes]
rs844161	0.82[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs893831	0.82[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs893832	0.84[ASN][1000 genomes]
rs9858954	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9859711	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9879927	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1003922	chr3:98410967-98453602	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv536662	chr3:98410967-98453602	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv470783	chr3:98431225-98466222	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3755569	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98443800-98450800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:98444000-98450800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:98447600-98450000	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr3:98447800-98450800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr3:98448000-98450600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:98448200-98450400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:98448400-98449800	Enhancers	GM12878-XiMat	blood
8	chr3:98448400-98450600	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr3:98448400-98450600	Enhancers	HUVEC	blood vessel
10	chr3:98448600-98450000	Enhancers	NHEK	skin
11	chr3:98448600-98450600	Weak transcription	Brain Angular Gyrus	brain
12	chr3:98448600-98450800	Enhancers	Primary hematopoietic stem cells	blood
13	chr3:98448600-98450800	Enhancers	HMEC	breast
14	chr3:98449200-98449800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:98449200-98449800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:98449200-98449800	Enhancers	Brain Anterior Caudate	brain
17	chr3:98449200-98449800	Enhancers	Thymus	Thymus
18	chr3:98449200-98449800	Enhancers	NH-A	brain
19	chr3:98449200-98450000	Enhancers	Osteobl	bone
20	chr3:98449200-98450400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:98449200-98450600	Enhancers	Adipose Nuclei	Adipose
22	chr3:98449400-98449800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
23	chr3:98449400-98449800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr3:98449400-98450600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:98449400-98450600	Weak transcription	Fetal Thymus	thymus
26	chr3:98449400-98450600	Enhancers	HepG2	liver
27	chr3:98449400-98451000	Weak transcription	Spleen	Spleen
28	chr3:98449600-98449800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
29	chr3:98449600-98449800	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr3:98449600-98449800	Enhancers	Right Atrium	heart
31	chr3:98449600-98449800	Enhancers	HSMM	muscle
32	chr3:98449600-98450000	Weak transcription	Pancreas	Pancrea
33	chr3:98449600-98450200	Weak transcription	Brain Hippocampus Middle	brain
34	chr3:98449600-98450400	Weak transcription	Aorta	Aorta
35	chr3:98449600-98450600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:98449600-98450600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:98449600-98450600	Enhancers	Dnd41	blood

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