Variant report

Variant	rs12442713
Chromosome Location	chr15:40280766-40280767
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10518676	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs10851392	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs11632930	0.92[GIH][hapmap]
rs11633416	0.88[CEU][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs12324733	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs12438989	0.87[EUR][1000 genomes]
rs12439021	0.87[EUR][1000 genomes]
rs12439335	0.88[CEU][hapmap]
rs12441927	0.87[EUR][1000 genomes]
rs12442731	0.94[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs12903784	0.81[EUR][1000 genomes]
rs12906976	0.87[EUR][1000 genomes]
rs16970134	0.88[ASN][1000 genomes]
rs2279579	0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs28541444	0.82[EUR][1000 genomes]
rs28696728	0.82[EUR][1000 genomes]
rs2934194	0.80[CEU][hapmap];0.87[GIH][hapmap]
rs3207297	0.86[TSI][hapmap]
rs34298786	0.87[EUR][1000 genomes]
rs4924402	0.83[CHD][hapmap]
rs552251	0.80[CEU][hapmap]
rs7173315	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7175589	0.80[ASN][1000 genomes]
rs8030025	0.88[CEU][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs8030640	0.80[CEU][hapmap];0.87[GIH][hapmap]
rs8030980	0.92[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.83[ASN][1000 genomes]
rs8034362	0.82[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8035930	0.85[EUR][1000 genomes]
rs8042788	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv428635	chr15:40274500-40436293	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12442713	GCHFR	cis	cerebellum	SCAN
rs12442713	EIF2AK4	cis	cerebellum	SCAN
rs12442713	EIF2AK4	cis	lesional skin	skin_eQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40227400-40283400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:40228200-40323800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr15:40236600-40303000	Weak transcription	Small Intestine	intestine
4	chr15:40249000-40304800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr15:40250000-40294800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr15:40250200-40299600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr15:40260800-40303400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr15:40262600-40293800	Weak transcription	Stomach Mucosa	stomach
9	chr15:40266400-40281800	Weak transcription	K562	blood
10	chr15:40269000-40284800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr15:40269000-40293200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:40269000-40293200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr15:40269200-40282000	Weak transcription	Esophagus	oesophagus
14	chr15:40269200-40283000	Weak transcription	Psoas Muscle	Psoas
15	chr15:40269400-40281600	Weak transcription	Colonic Mucosa	Colon
16	chr15:40269400-40283000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:40269600-40282400	Weak transcription	Fetal Brain Male	brain
18	chr15:40269600-40295600	Weak transcription	Fetal Heart	heart
19	chr15:40269800-40285400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr15:40270400-40282400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr15:40276400-40295600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr15:40277600-40287400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:40277600-40288000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr15:40277600-40288000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:40277600-40288400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:40277600-40294600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr15:40277600-40303600	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr15:40277600-40303800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:40277600-40304400	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr15:40277800-40281400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr15:40277800-40283800	Strong transcription	HUVEC	blood vessel
32	chr15:40277800-40284200	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr15:40277800-40285800	Strong transcription	Brain Cingulate Gyrus	brain
34	chr15:40277800-40286000	Strong transcription	Brain Anterior Caudate	brain
35	chr15:40277800-40286600	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr15:40277800-40286600	Strong transcription	A549	lung
37	chr15:40277800-40286600	Strong transcription	Dnd41	blood
38	chr15:40277800-40286600	Strong transcription	HSMM	muscle
39	chr15:40277800-40286600	Strong transcription	NHDF-Ad	bronchial
40	chr15:40277800-40286600	Strong transcription	NHEK	skin
41	chr15:40277800-40286600	Strong transcription	Osteobl	bone
42	chr15:40277800-40286800	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr15:40277800-40287000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr15:40277800-40287600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:40277800-40287800	Strong transcription	Rectal Smooth Muscle	rectum
46	chr15:40277800-40288000	Strong transcription	HMEC	breast
47	chr15:40277800-40288200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:40277800-40288400	Strong transcription	NH-A	brain
49	chr15:40277800-40288600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr15:40277800-40288800	Strong transcription	Placenta	Placenta

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