Variant report

Variant	rs2740169
Chromosome Location	chr1:226021103-226021104
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	chr1:225839806..225841875-chr1:226019865..226022618,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154380	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs2740168	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv947519	chr1:225998770-226034631	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv945328	chr1:226015604-226031170	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv873231	chr1:226019653-226134471	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2740169	EPHX1	cis	brain	BrainEAC
rs2740169	EPHX1	cis	hippocampus	BrainEAC

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226006200-226022000	Weak transcription	NHDF-Ad	bronchial
2	chr1:226013400-226031800	Weak transcription	Fetal Kidney	kidney
3	chr1:226013600-226052600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:226013800-226032000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:226013800-226037200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:226014000-226032800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:226014400-226021200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:226014600-226022400	Weak transcription	Right Atrium	heart
9	chr1:226014600-226035600	Weak transcription	Small Intestine	intestine
10	chr1:226014800-226047800	Weak transcription	Psoas Muscle	Psoas
11	chr1:226015000-226022400	Weak transcription	Right Ventricle	heart
12	chr1:226015000-226022400	Weak transcription	Stomach Mucosa	stomach
13	chr1:226015400-226026400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:226015400-226032400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:226015400-226033200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:226015600-226021400	Strong transcription	Stomach Smooth Muscle	stomach
17	chr1:226015600-226033600	Weak transcription	K562	blood
18	chr1:226016000-226051000	Weak transcription	NH-A	brain
19	chr1:226016400-226021400	Strong transcription	Brain Hippocampus Middle	brain
20	chr1:226016400-226022000	Strong transcription	Fetal Stomach	stomach
21	chr1:226016400-226033400	Strong transcription	Fetal Intestine Small	intestine
22	chr1:226016600-226021400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:226016600-226021400	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr1:226016600-226021400	Strong transcription	Lung	lung
25	chr1:226016600-226023800	Genic enhancers	Liver	Liver
26	chr1:226016800-226021200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:226016800-226021200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:226016800-226021200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:226016800-226021200	Strong transcription	Fetal Muscle Trunk	muscle
30	chr1:226016800-226021400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:226016800-226022400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:226016800-226033600	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr1:226017000-226021400	Strong transcription	Colon Smooth Muscle	Colon
34	chr1:226017000-226022400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:226017200-226021400	Strong transcription	Adipose Nuclei	Adipose
36	chr1:226017200-226022400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:226017400-226049800	Weak transcription	HUVEC	blood vessel
38	chr1:226018000-226021400	Strong transcription	A549	lung
39	chr1:226018000-226022400	Weak transcription	Gastric	stomach
40	chr1:226018400-226022400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:226018600-226025800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:226019000-226021200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:226019000-226021400	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:226019000-226021600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:226019200-226021200	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr1:226019200-226021200	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:226019200-226021200	Strong transcription	Brain Substantia Nigra	brain
48	chr1:226019200-226021200	Strong transcription	Rectal Smooth Muscle	rectum
49	chr1:226019200-226021400	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr1:226019200-226021600	Strong transcription	Esophagus	oesophagus

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