Variant report

Variant	rs10954577
Chromosome Location	chr7:136914815-136914816
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10954576	0.89[TSI][hapmap]
rs11505752	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11561959	0.81[CEU][hapmap];0.86[TSI][hapmap]
rs1376610	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1376611	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1579354	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17168991	0.92[YRI][hapmap];0.82[AFR][1000 genomes]
rs17168993	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17168999	0.82[MKK][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs1725022	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2693652	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56866301	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs832975	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs832983	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[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	nsv1029192	chr7:136433278-137147566	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv831149	chr7:136831665-137006468	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv608464	chr7:136882925-136935459	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv608465	chr7:136888610-136935459	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10954577	WDR91	cis	parietal	SCAN
rs10954577	STRA8	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:136901600-136922800	Strong transcription	Cortex derived primary cultured neurospheres	brain
2	chr7:136902000-136933800	Weak transcription	Fetal Brain Female	brain
3	chr7:136902200-136915800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr7:136906600-136925200	Weak transcription	Fetal Stomach	stomach
5	chr7:136909200-136922600	Weak transcription	Brain Hippocampus Middle	brain
6	chr7:136909600-136935800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr7:136909800-136926200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr7:136909800-136943000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr7:136911000-136922400	Weak transcription	Brain Substantia Nigra	brain
10	chr7:136911000-136927000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr7:136911200-136925800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr7:136911600-136936400	Weak transcription	Fetal Heart	heart
13	chr7:136911800-136920800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr7:136912400-136922800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr7:136913400-136915000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr7:136913400-136937200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr7:136913800-136918400	Strong transcription	H9 Derived Neuronal Progenitor 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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