Variant report

Variant	rs13436644
Chromosome Location	chr5:36608101-36608102
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	MAX	chr5:36608002-36608744	Hela-S3	cervix:	n/a	chr5:36608255-36608266 chr5:36608257-36608266 chr5:36608247-36608263 chr5:36608252-36608267
2	MYC	chr5:36606294-36608545	MCF10A-Er-Src	breast:	n/a	chr5:36608255-36608266 chr5:36608257-36608266 chr5:36608247-36608263 chr5:36606708-36606718 chr5:36608252-36608267
3	RCOR1	chr5:36607998-36608867	Hela-S3	cervix:	n/a	n/a
4	CEBPB	chr5:36607944-36608821	Hela-S3	cervix:	n/a	chr5:36608334-36608347 chr5:36608334-36608345 chr5:36608334-36608347 chr5:36608335-36608346
5	MXI1	chr5:36606408-36608431	Hela-S3	cervix:	n/a	chr5:36608257-36608266
6	CEBPB	chr5:36608055-36608520	H1-hESC	embryonic stem cell:	n/a	chr5:36608334-36608347 chr5:36608334-36608345 chr5:36608334-36608347 chr5:36608335-36608346
7	POLR2A	chr5:36606395-36608414	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:36607368..36609529-chr5:36613052..36615679,2	MCF-7	breast:

Variant related genes	Relation type
SLC1A3	TF binding region
ENSG00000079215	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10078147	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1428972	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2562575	0.92[CEU][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes]
rs2562576	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2562577	0.92[CEU][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes]
rs2562578	0.91[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs2562579	0.91[EUR][1000 genomes]
rs2562580	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2562581	0.92[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2731878	0.92[CEU][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes]
rs2731879	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs2731883	0.91[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs2731884	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2731886	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3814068	0.87[EUR][1000 genomes]
rs4591778	1.00[CEU][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492319	chr5:36570707-37061019	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv881025	chr5:36575021-36613053	Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
3	nsv830263	chr5:36576504-36755093	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2762516	chr5:36599385-36613201	Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13436644	EGFLAM	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36604800-36612000	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr5:36605400-36608200	Active TSS	NHDF-Ad	bronchial
3	chr5:36605400-36608400	Active TSS	Brain Anterior Caudate	brain
4	chr5:36605400-36612800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr5:36605600-36608600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:36605600-36609800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr5:36605600-36609800	Active TSS	Brain Hippocampus Middle	brain
8	chr5:36605800-36608200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr5:36605800-36608200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:36605800-36608600	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr5:36605800-36611200	Active TSS	Right Atrium	heart
12	chr5:36606000-36608200	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr5:36606000-36608200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr5:36606000-36608200	Active TSS	Brain Angular Gyrus	brain
15	chr5:36606000-36608200	Active TSS	Placenta	Placenta
16	chr5:36606000-36608200	Active TSS	Ovary	ovary
17	chr5:36606000-36608200	Active TSS	HSMMtube	muscle
18	chr5:36606000-36608400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
19	chr5:36606000-36608400	Bivalent/Poised TSS	Fetal Lung	lung
20	chr5:36606000-36609200	Active TSS	Brain Substantia Nigra	brain
21	chr5:36606000-36609200	Active TSS	Fetal Heart	heart
22	chr5:36606000-36609200	Active TSS	Psoas Muscle	Psoas
23	chr5:36606000-36609400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:36606000-36610400	Active TSS	Right Ventricle	heart
25	chr5:36606200-36608200	Active TSS	H1 Cell Line	embryonic stem cell
26	chr5:36606200-36608200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
27	chr5:36606200-36608400	Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr5:36606200-36608400	Active TSS	HSMM	muscle
29	chr5:36606200-36608600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr5:36606200-36608600	Active TSS	H9 Cell Line	embryonic stem cell
31	chr5:36606200-36608800	Active TSS	Esophagus	oesophagus
32	chr5:36606200-36610000	Active TSS	Brain Cingulate Gyrus	brain
33	chr5:36606200-36610400	Active TSS	Left Ventricle	heart
34	chr5:36606200-36611000	Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr5:36606400-36608200	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr5:36606400-36608400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr5:36606400-36608800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr5:36606400-36612000	Active TSS	Fetal Brain Female	brain
39	chr5:36606600-36608400	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr5:36606600-36608800	Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr5:36606800-36610400	Active TSS	Brain Germinal Matrix	brain
42	chr5:36607000-36610800	Active TSS	Fetal Brain Male	brain
43	chr5:36607200-36608800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:36607200-36608800	Flanking Active TSS	Hela-S3	cervix
45	chr5:36607400-36608600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr5:36607600-36608400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr5:36607600-36608600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr5:36607600-36608600	Active TSS	Fetal Muscle Trunk	muscle
49	chr5:36607600-36608800	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr5:36607800-36608200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links