Variant report

Variant	rs9313204
Chromosome Location	chr5:7823576-7823577
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:7822314..7823878-chr5:7829046..7830943,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10474820	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10474821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10475395	0.96[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs162054	0.85[EUR][1000 genomes]
rs16879202	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]
rs16879204	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs179044	0.85[EUR][1000 genomes]
rs191261	0.88[CEU][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2287778	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs326171	0.88[CEU][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.86[EUR][1000 genomes]
rs326173	0.88[CEU][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap];0.86[EUR][1000 genomes]
rs326174	0.88[CEU][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap];0.86[EUR][1000 genomes]
rs326175	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs326184	0.84[EUR][1000 genomes]
rs4702502	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66820699	0.86[EUR][1000 genomes]
rs6870733	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6879836	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6887726	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7703102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs989632	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs989633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs989634	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs989635	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	esv3354956	chr5:7823152-7827350	Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9313204	SEMA5A	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:7803800-7824800	Weak transcription	Aorta	Aorta
2	chr5:7806000-7823600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr5:7808400-7827000	Weak transcription	Brain Substantia Nigra	brain
4	chr5:7816400-7825200	Weak transcription	Fetal Intestine Small	intestine
5	chr5:7816600-7827000	Weak transcription	Ovary	ovary
6	chr5:7816800-7827400	Weak transcription	Brain Hippocampus Middle	brain
7	chr5:7816800-7828800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr5:7817000-7826800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr5:7817000-7828000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:7817200-7825200	Weak transcription	Pancreas	Pancrea
11	chr5:7817200-7826400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr5:7817400-7824800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:7817800-7825200	Weak transcription	Gastric	stomach
14	chr5:7818400-7828200	Weak transcription	Fetal Brain Female	brain
15	chr5:7818800-7823600	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr5:7819200-7829200	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr5:7820000-7830200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr5:7820200-7824400	Weak transcription	Fetal Stomach	stomach
19	chr5:7820200-7824800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr5:7820200-7828400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:7820800-7825000	Weak transcription	Esophagus	oesophagus
22	chr5:7821400-7825800	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:7821600-7823600	Strong transcription	Brain Inferior Temporal Lobe	brain
24	chr5:7821600-7823800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr5:7822000-7824600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr5:7822000-7825200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr5:7822000-7828600	Weak transcription	Brain Angular Gyrus	brain
28	chr5:7822000-7829000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr5:7822200-7826400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr5:7822200-7827000	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr5:7822200-7828200	Weak transcription	Brain Anterior Caudate	brain
32	chr5:7822400-7824600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr5:7823000-7824400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr5:7823000-7824600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr5:7823200-7824600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr5:7823400-7826400	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links