Variant report

Variant	rs12440899
Chromosome Location	chr15:40340291-40340292
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:40339870..40341521-chr15:40394237..40395838,2	MCF-7	breast:
2	chr15:40340027..40343155-chr15:40345939..40349280,3	K562	blood:
3	chr15:40336254..40340864-chr15:40394731..40398446,8	MCF-7	breast:
4	chr15:40339902..40342290-chr15:40395985..40398668,2	MCF-7	breast:
5	chr15:40338671..40341082-chr15:40391017..40392708,2	MCF-7	breast:
6	chr15:40337627..40341020-chr15:40341608..40343639,3	K562	blood:
7	chr15:40336937..40340971-chr15:40343981..40345656,3	K562	blood:
8	chr15:40338929..40343184-chr15:40345688..40348186,4	MCF-7	breast:
9	chr15:40338471..40341053-chr15:40396995..40399108,2	K562	blood:
10	chr15:40340164..40343068-chr15:40383940..40387129,4	MCF-7	breast:
11	chr15:40339113..40341248-chr15:40387682..40389325,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000104081	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11638521	0.81[ASN][1000 genomes]
rs12441483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16970286	0.89[JPT][hapmap]
rs16970291	0.89[JPT][hapmap]
rs3803361	1.00[CEU][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4923848	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4923850	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4923851	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924412	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924414	1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162269	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7181230	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs7181985	0.84[CHB][hapmap];0.93[GIH][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7183386	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972424	0.89[JPT][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12440899	EIF2AK4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40336200-40343400	Enhancers	Fetal Heart	heart
2	chr15:40336600-40340600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:40336600-40341000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:40336600-40341000	Enhancers	HSMMtube	muscle
5	chr15:40336600-40341200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr15:40336600-40341800	Enhancers	Fetal Thymus	thymus
7	chr15:40336600-40342800	Enhancers	Spleen	Spleen
8	chr15:40336600-40343000	Enhancers	Primary B cells from peripheral blood	blood
9	chr15:40336800-40341000	Enhancers	Fetal Stomach	stomach
10	chr15:40336800-40341600	Enhancers	Placenta	Placenta
11	chr15:40336800-40342800	Enhancers	Primary B cells from cord blood	blood
12	chr15:40336800-40343400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr15:40337000-40340400	Enhancers	Stomach Mucosa	stomach
14	chr15:40337000-40340800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:40337000-40340800	Enhancers	Fetal Lung	lung
16	chr15:40337000-40340800	Enhancers	HMEC	breast
17	chr15:40337000-40340800	Enhancers	HUVEC	blood vessel
18	chr15:40337000-40340800	Enhancers	NHLF	lung
19	chr15:40337000-40342200	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr15:40337000-40344800	Enhancers	Primary T cells fromperipheralblood	blood
21	chr15:40337400-40342600	Enhancers	Primary hematopoietic stem cells	blood
22	chr15:40337400-40342600	Enhancers	Adipose Nuclei	Adipose
23	chr15:40337400-40343600	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr15:40337600-40340400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:40337600-40341000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr15:40337600-40341000	Enhancers	HSMM	muscle
27	chr15:40337600-40341200	Enhancers	Fetal Muscle Trunk	muscle
28	chr15:40337600-40342800	Weak transcription	Fetal Brain Male	brain
29	chr15:40337800-40340400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr15:40337800-40340400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr15:40337800-40340600	Genic enhancers	Fetal Intestine Small	intestine
32	chr15:40337800-40340600	Enhancers	A549	lung
33	chr15:40337800-40340600	Enhancers	NHDF-Ad	bronchial
34	chr15:40337800-40340800	Enhancers	Muscle Satellite Cultured Cells	--
35	chr15:40337800-40340800	Enhancers	Small Intestine	intestine
36	chr15:40337800-40341000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr15:40337800-40341400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:40337800-40343000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr15:40337800-40343000	Enhancers	Left Ventricle	heart
40	chr15:40337800-40355600	Weak transcription	Brain Angular Gyrus	brain
41	chr15:40337800-40355600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr15:40338000-40340600	Weak transcription	Brain Substantia Nigra	brain
43	chr15:40338000-40340800	Enhancers	NH-A	brain
44	chr15:40338000-40342200	Weak transcription	Psoas Muscle	Psoas
45	chr15:40338000-40343800	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr15:40338000-40345200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr15:40338000-40347000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:40338200-40342200	Weak transcription	K562	blood
49	chr15:40338200-40343000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr15:40338200-40345000	Weak transcription	H9 Cell Line	embryonic stem cell

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