Variant report

Variant	rs3784746
Chromosome Location	chr15:92935629-92935630
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	MAX	chr15:92935045-92935712	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:92927559..92930317-chr15:92934349..92936037,2	MCF-7	breast:

Variant related genes	Relation type
ST8SIA2	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs3759914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759916	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4238483	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4570781	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4583192	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4777968	0.95[CHB][hapmap];0.96[JPT][hapmap];0.95[ASN][1000 genomes]
rs6416575	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6496930	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs8025735	1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8035799	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs8040217	0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]

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	nsv948621	chr15:92688981-93158095	Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1049561	chr15:92758434-93097965	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1037972	chr15:92804908-93270761	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3784746	ST8SIA2	cis	multi-tissue	Pritchard

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:92935000-92936400	Enhancers	Fetal Brain Male	brain
2	chr15:92935200-92935800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
3	chr15:92935200-92935800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
4	chr15:92935200-92936400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:92935200-92936400	Bivalent Enhancer	Fetal Thymus	thymus
6	chr15:92935400-92935800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
7	chr15:92935400-92935800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:92935400-92935800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
9	chr15:92935400-92936400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
10	chr15:92935400-92936400	Bivalent Enhancer	Fetal Muscle Leg	muscle
11	chr15:92935400-92936600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr15:92935400-92936600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
13	chr15:92935400-92936600	Flanking Active TSS	Brain Germinal Matrix	brain
14	chr15:92935400-92938400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
15	chr15:92935400-92938800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
16	chr15:92935600-92935800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
17	chr15:92935600-92935800	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr15:92935600-92936000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:92935600-92936200	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
20	chr15:92935600-92936200	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr15:92935600-92936400	Bivalent Enhancer	Fetal Stomach	stomach
22	chr15:92935600-92936600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:92935600-92936600	Flanking Active TSS	Fetal Brain Female	brain
24	chr15:92935600-92936600	Bivalent Enhancer	NHDF-Ad	bronchial
25	chr15:92935600-92936800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell

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