Variant report

Variant	rs1869774
Chromosome Location	chr15:93010177-93010178
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11634493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12708594	0.86[LWK][hapmap];0.83[MEX][hapmap]
rs7163161	0.83[MEX][hapmap]
rs7168443	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs897466	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1869774	RHCG	cis	parietal	SCAN
rs1869774	FANCI	cis	parietal	SCAN
rs1869774	SV2B	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:92972000-93011800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:92972800-93011400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:92973400-93012200	Strong transcription	Brain Germinal Matrix	brain
4	chr15:92973600-93011400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr15:92982400-93011800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:92997400-93011400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:93000800-93013200	Strong transcription	Fetal Brain Female	brain
8	chr15:93001400-93015800	Weak transcription	Fetal Brain Male	brain
9	chr15:93005800-93010200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr15:93007000-93010200	Strong transcription	Fetal Muscle Leg	muscle
11	chr15:93007200-93011200	Strong transcription	Fetal Stomach	stomach
12	chr15:93008400-93014400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr15:93008800-93011000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:93009800-93010800	Weak transcription	HSMMtube	muscle
15	chr15:93009800-93011200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr15:93009800-93013400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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