Variant report

Variant	rs2358994
Chromosome Location	chr1:114429461-114429462
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:114429070..114435293-chr1:114435414..114441720,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134262	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10745340	0.80[MEX][hapmap]
rs10776775	0.80[MEX][hapmap]
rs11102691	0.83[MEX][hapmap]
rs11102694	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11102701	0.88[EUR][1000 genomes]
rs11102702	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11552449	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12046289	0.80[AMR][1000 genomes]
rs1217392	0.80[MEX][hapmap]
rs1217413	1.00[ASW][hapmap]
rs2358816	0.84[CHB][hapmap]
rs2358995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2359167	1.00[ASW][hapmap]
rs2488457	1.00[ASW][hapmap]
rs3761936	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7513707	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7547478	0.90[CHB][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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2358994	MAGI3	cis	parietal	SCAN
rs2358994	CTTNBP2NL	cis	parietal	SCAN
rs2358994	PHTF1	cis	parietal	SCAN
rs2358994	MAGI3	cis	cerebellum	SCAN
rs2358994	PHTF1	cis	cerebellum	SCAN
rs2358994	KCNA10	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114415000-114447000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:114415400-114437000	Weak transcription	Thymus	Thymus
3	chr1:114417200-114437000	Weak transcription	Primary B cells from cord blood	blood
4	chr1:114420200-114437800	Weak transcription	Brain Hippocampus Middle	brain
5	chr1:114420200-114446400	Weak transcription	Aorta	Aorta
6	chr1:114421800-114429600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:114423400-114429600	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr1:114423600-114436000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:114424000-114429800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:114424200-114429800	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr1:114424200-114437800	Weak transcription	Brain Germinal Matrix	brain
12	chr1:114424400-114436200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:114424600-114430000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr1:114424600-114431200	Weak transcription	Small Intestine	intestine
15	chr1:114424600-114433200	Weak transcription	GM12878-XiMat	blood
16	chr1:114424600-114436400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:114424600-114436600	Weak transcription	Fetal Thymus	thymus
18	chr1:114424600-114437800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr1:114424600-114438800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:114424600-114442400	Weak transcription	Psoas Muscle	Psoas
21	chr1:114424800-114429800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:114424800-114430200	Weak transcription	Dnd41	blood
23	chr1:114425000-114436800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr1:114425200-114436200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr1:114425400-114436400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:114425400-114437400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:114425600-114436400	Weak transcription	Brain Substantia Nigra	brain
28	chr1:114426400-114431800	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr1:114426800-114429800	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr1:114427200-114436800	Weak transcription	Fetal Brain Female	brain
31	chr1:114427400-114430400	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr1:114427400-114437000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:114427600-114437800	Weak transcription	Brain Angular Gyrus	brain
34	chr1:114427800-114432000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:114428200-114430000	Active TSS	Gastric	stomach
36	chr1:114428200-114437000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:114428200-114437800	Weak transcription	Lung	lung
38	chr1:114428400-114429800	Weak transcription	NHEK	skin
39	chr1:114428400-114430200	Active TSS	Duodenum Mucosa	Duodenum
40	chr1:114428400-114430400	Active TSS	Rectal Mucosa Donor 31	rectum
41	chr1:114428600-114437800	Weak transcription	Esophagus	oesophagus
42	chr1:114428800-114429800	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr1:114428800-114430000	Active TSS	Colonic Mucosa	Colon
44	chr1:114428800-114430000	Active TSS	Rectal Smooth Muscle	rectum
45	chr1:114428800-114430400	Active TSS	Fetal Intestine Large	intestine
46	chr1:114428800-114430400	Active TSS	Fetal Intestine Small	intestine
47	chr1:114428800-114430600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr1:114428800-114430800	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr1:114428800-114430800	Active TSS	Stomach Mucosa	stomach
50	chr1:114429000-114430000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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