Variant report

Variant	rs16879202
Chromosome Location	chr5:7828966-7828967
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10474820	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10474821	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10475395	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs162054	0.87[EUR][1000 genomes]
rs16879204	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs179044	0.87[EUR][1000 genomes]
rs191261	0.85[CEU][hapmap];0.91[CHD][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2287778	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326171	0.85[CEU][hapmap];0.88[CHD][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs326173	0.85[CEU][hapmap];0.93[CHD][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs326174	0.85[CEU][hapmap];0.93[CHD][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs326175	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326184	0.86[EUR][1000 genomes]
rs4702502	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66820699	0.86[EUR][1000 genomes]
rs6870733	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6879836	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6887726	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7703102	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9313204	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs989632	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs989633	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs989634	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs989635	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[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	nsv916892	chr5:7634377-8158890	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS 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	19 gene(s)	inside rSNPs	diseases
2	nsv949492	chr5:7682909-7953909	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv533983	chr5:7701457-8275379	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv461927	chr5:7757812-7854289	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv597004	chr5:7757812-7854289	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16879202	SEMA5A	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:7819200-7829200	Strong transcription	Skeletal Muscle Female	skeletal muscle
2	chr5:7820000-7830200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:7822000-7829000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:7825600-7829200	Weak transcription	Gastric	stomach
5	chr5:7825600-7830200	Weak transcription	Aorta	Aorta
6	chr5:7827200-7829000	Weak transcription	Fetal Intestine Small	intestine
7	chr5:7827400-7829200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr5:7827400-7829200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:7827400-7829200	Enhancers	Brain Germinal Matrix	brain
10	chr5:7827400-7829200	Enhancers	Brain Hippocampus Middle	brain
11	chr5:7827600-7829400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr5:7827600-7829400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr5:7827600-7829400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr5:7827600-7829400	Weak transcription	Ovary	ovary
15	chr5:7827600-7829800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr5:7827600-7830200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr5:7827600-7830600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr5:7827600-7831000	Weak transcription	Fetal Stomach	stomach
19	chr5:7827600-7833600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr5:7827600-7834000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr5:7827800-7830000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr5:7828000-7829000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:7828200-7829200	Enhancers	Brain Anterior Caudate	brain
24	chr5:7828200-7833600	Weak transcription	Fetal Brain Male	brain
25	chr5:7828400-7839000	Weak transcription	Fetal Brain Female	brain
26	chr5:7828600-7829000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr5:7828600-7829000	Enhancers	HSMM	muscle
28	chr5:7828600-7829400	Enhancers	Brain Substantia Nigra	brain
29	chr5:7828800-7829000	Enhancers	Pancreas	Pancrea

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