Variant report

Variant	rs1530655
Chromosome Location	chr3:98477091-98477092
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98475526..98478052-chr3:98486297..98488947,2	MCF-7	breast:
2	chr3:98475428..98477221-chr3:98477568..98479481,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10470451	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs115931	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs11923134	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12494828	0.81[EUR][1000 genomes]
rs12496694	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13315676	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1440149	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1440155	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1440158	0.87[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1868217	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs278370	0.81[JPT][hapmap]
rs278374	0.91[CHB][hapmap];0.86[YRI][hapmap];0.85[ASN][1000 genomes]
rs28553326	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28707457	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3755569	0.87[CEU][hapmap];0.91[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3755570	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3772091	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4638909	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56976804	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60464352	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62276459	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62278471	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62278472	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7611040	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7614161	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7620634	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7620636	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7628381	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7630887	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7631062	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7643537	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7649812	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7652790	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs828593	0.80[ASN][1000 genomes]
rs828594	0.87[CHB][hapmap]
rs828595	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs828596	0.91[CHB][hapmap];0.83[YRI][hapmap];0.85[ASN][1000 genomes]
rs828597	0.91[CHB][hapmap];0.82[YRI][hapmap];0.85[ASN][1000 genomes]
rs828598	0.91[CHB][hapmap];0.82[YRI][hapmap]
rs828599	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs828602	0.85[ASN][1000 genomes]
rs828613	0.83[ASN][1000 genomes]
rs844161	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs893831	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs893832	0.83[ASN][1000 genomes]
rs9858954	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9859711	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9879927	0.87[CEU][hapmap];0.95[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1530655	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98454400-98478000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:98456600-98479600	Weak transcription	Dnd41	blood
3	chr3:98463400-98481600	Weak transcription	Right Ventricle	heart
4	chr3:98463800-98477400	Weak transcription	Brain Substantia Nigra	brain
5	chr3:98469600-98480600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:98469800-98479000	Weak transcription	Right Atrium	heart
7	chr3:98469800-98480800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr3:98469800-98481800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:98469800-98481800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:98469800-98482200	Weak transcription	Psoas Muscle	Psoas
11	chr3:98470000-98481800	Weak transcription	Aorta	Aorta
12	chr3:98470000-98482600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:98470200-98477800	Weak transcription	Left Ventricle	heart
14	chr3:98470200-98480200	Weak transcription	Thymus	Thymus
15	chr3:98473600-98477400	Weak transcription	GM12878-XiMat	blood
16	chr3:98475200-98477400	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:98475200-98477800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:98475200-98478200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:98475200-98480200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:98475400-98479000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:98475400-98489400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:98475600-98479000	Weak transcription	Placenta	Placenta
23	chr3:98475600-98480000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr3:98476200-98477800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:98476400-98489400	Weak transcription	HepG2	liver
26	chr3:98477000-98477600	Enhancers	HUVEC	blood vessel
27	chr3:98477000-98490200	Enhancers	Fetal Heart	heart

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