Variant report

Variant	rs2562577
Chromosome Location	chr5:36603350-36603351
allele	G/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	CTCF	chr5:36602746-36603386	HCT-116	colon:	n/a	n/a
2	MXI1	chr5:36602953-36603369	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr5:36602897-36603399	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr5:36602704-36603472	HCT-116	colon:	n/a	n/a
5	CTCF	chr5:36602822-36603444	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr5:36603220-36603370	Caco-2	colon:	n/a	n/a
7	MAX	chr5:36602803-36603523	H1-hESC	embryonic stem cell:	n/a	chr5:36602807-36602816 chr5:36602807-36602816 chr5:36602807-36602816
8	RAD21	chr5:36602825-36603403	H1-hESC	embryonic stem cell:	n/a	n/a
9	RAD21	chr5:36602718-36603494	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:36602958..36603570-chr5:36688895..36689448,2	MCF-7	breast:
2	chr5:36602570..36603716-chr5:36690159..36691138,5	MCF-7	breast:
3	chr5:36602536..36603410-chr5:36692728..36693815,5	MCF-7	breast:
4	chr5:36602557..36603415-chr5:36695863..36696651,3	MCF-7	breast:

Variant related genes	Relation type
SLC1A3	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10078147	0.92[CEU][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes]
rs13436644	0.92[CEU][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes]
rs1428972	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2562575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562576	1.00[CEU][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2562578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562579	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2562580	1.00[CEU][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2562581	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2731878	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2731879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2731883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2731884	1.00[CEU][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2731886	1.00[CEU][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3814068	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4591778	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7730144	0.96[YRI][hapmap]

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
rs2562577	EGFLAM	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36591200-36606200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:36597000-36605600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:36597000-36606200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr5:36597200-36605200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr5:36598400-36604400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr5:36600000-36604200	Enhancers	Brain Angular Gyrus	brain
7	chr5:36600000-36605600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:36600200-36605600	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr5:36600200-36606000	Enhancers	Brain Substantia Nigra	brain
10	chr5:36601000-36604600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr5:36601000-36605000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr5:36601000-36605800	Weak transcription	Adipose Nuclei	Adipose
13	chr5:36601200-36605400	Weak transcription	NHEK	skin
14	chr5:36601200-36605600	Weak transcription	HMEC	breast
15	chr5:36601200-36605800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:36601200-36606000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:36601400-36605200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr5:36601600-36604800	Weak transcription	NHDF-Ad	bronchial
19	chr5:36601800-36604200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:36601800-36605200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr5:36601800-36605200	Enhancers	Brain Hippocampus Middle	brain
22	chr5:36601800-36605800	Weak transcription	Fetal Stomach	stomach
23	chr5:36601800-36606000	Weak transcription	NHLF	lung
24	chr5:36602000-36606200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr5:36602200-36605400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr5:36602200-36605800	Weak transcription	Fetal Brain Female	brain
27	chr5:36602200-36606200	Weak transcription	Pancreas	Pancrea
28	chr5:36602600-36604600	Enhancers	Brain Anterior Caudate	brain
29	chr5:36602800-36603400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr5:36602800-36603600	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr5:36602800-36603600	Enhancers	Left Ventricle	heart
32	chr5:36602800-36603800	Enhancers	Brain Cingulate Gyrus	brain
33	chr5:36603000-36603400	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr5:36603000-36603400	Enhancers	H1 Cell Line	embryonic stem cell
35	chr5:36603000-36603400	Enhancers	H9 Cell Line	embryonic stem cell
36	chr5:36603000-36603400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr5:36603000-36603400	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr5:36603000-36603400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr5:36603000-36604400	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr5:36603200-36603400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr5:36603200-36603600	Enhancers	Fetal Muscle Leg	muscle

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