Variant report

Variant	rs3207297
Chromosome Location	chr15:40313141-40313142
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:40313127-40314634	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
EIF2AK4	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11629915	0.94[ASN][1000 genomes]
rs11633416	0.81[TSI][hapmap]
rs11635537	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635600	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442713	0.86[TSI][hapmap]
rs12591842	0.90[GIH][hapmap];0.81[MKK][hapmap]
rs12903784	0.95[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2279579	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2412463	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2898973	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs35697496	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8034362	0.88[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.82[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3207297	EIF2AK4	Cis_1M	lymphoblastoid	RTeQTL
rs3207297	EIF2AK4	cis	cerebellum	SCAN
rs3207297	C15orf24	cis	cerebellum	SCAN
rs3207297	EIF2AK4	cis	lesional skin	skin_eQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40228200-40323800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr15:40293000-40315000	Strong transcription	Stomach Smooth Muscle	stomach
3	chr15:40296400-40313200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr15:40296400-40325200	Weak transcription	Hela-S3	cervix
5	chr15:40301000-40322000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr15:40301200-40313200	Weak transcription	Fetal Heart	heart
7	chr15:40303000-40329600	Strong transcription	Liver	Liver
8	chr15:40303800-40320600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr15:40305200-40330200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr15:40306800-40313800	Strong transcription	Adipose Nuclei	Adipose
11	chr15:40306800-40313800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr15:40306800-40315200	Strong transcription	NHEK	skin
13	chr15:40306800-40319200	Strong transcription	Fetal Intestine Large	intestine
14	chr15:40306800-40319600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr15:40306800-40328800	Weak transcription	Stomach Mucosa	stomach
16	chr15:40306800-40329800	Strong transcription	Osteobl	bone
17	chr15:40307000-40315000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr15:40307000-40315400	Strong transcription	Fetal Stomach	stomach
19	chr15:40307000-40318600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:40307000-40329000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr15:40307000-40329400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr15:40307200-40315400	Strong transcription	Fetal Muscle Leg	muscle
23	chr15:40307200-40329600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr15:40307400-40313600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr15:40307400-40326800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:40307400-40329600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr15:40307600-40314800	Strong transcription	Primary hematopoietic stem cells	blood
28	chr15:40307600-40314800	Strong transcription	Placenta	Placenta
29	chr15:40307600-40317400	Strong transcription	HUVEC	blood vessel
30	chr15:40307600-40319000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr15:40307600-40326200	Strong transcription	HSMM	muscle
32	chr15:40307600-40329200	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr15:40307600-40329200	Strong transcription	HMEC	breast
34	chr15:40307800-40313800	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr15:40307800-40315400	Strong transcription	Fetal Intestine Small	intestine
36	chr15:40307800-40329600	Strong transcription	NH-A	brain
37	chr15:40307800-40330000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr15:40308000-40314000	Strong transcription	Primary B cells from cord blood	blood
39	chr15:40308000-40329000	Strong transcription	HepG2	liver
40	chr15:40308000-40329600	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr15:40308000-40329800	Strong transcription	NHDF-Ad	bronchial
42	chr15:40308000-40330000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr15:40308200-40315000	Strong transcription	Lung	lung
44	chr15:40308200-40318200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
45	chr15:40308200-40319000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr15:40308200-40329600	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr15:40308400-40315600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr15:40308600-40314000	Weak transcription	GM12878-XiMat	blood
49	chr15:40308600-40328800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr15:40308600-40330000	Strong transcription	HUES6 Cell Line	embryonic stem cell

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