Variant report

Variant	rs10025804
Chromosome Location	chr4:187590946-187590947
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:187589219..187591473-chr4:187596376..187599328,2	MCF-7	breast:
2	chr4:187590589..187591501-chr4:187640709..187641388,2	MCF-7	breast:
3	chr4:187590133..187593281-chr4:187645250..187648051,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000083857	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs327076	0.80[CEU][hapmap]
rs327080	0.87[CEU][hapmap];0.98[GIH][hapmap];0.81[TSI][hapmap]
rs327081	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs327082	0.91[CEU][hapmap];0.96[YRI][hapmap];0.80[EUR][1000 genomes]
rs370357	0.83[ASW][hapmap];0.91[CEU][hapmap];0.95[GIH][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap]
rs3733414	0.83[CHB][hapmap]
rs458021	0.83[CHB][hapmap]
rs462422	0.91[CEU][hapmap];0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025088	chr4:187407683-187674585	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1025244	chr4:187419770-188284813	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1034212	chr4:187437895-188030805	Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv537438	chr4:187437895-188030805	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1015619	chr4:187442453-187595058	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1023800	chr4:187444255-187593799	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv532745	chr4:187471692-188205443	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv1022262	chr4:187475862-187848284	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv1024705	chr4:187534005-187849091	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1026970	chr4:187537418-187913351	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv596440	chr4:187538133-187848075	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv881509	chr4:187574398-187614434	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10025804	ACSL1	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:187573000-187605400	Weak transcription	Gastric	stomach
2	chr4:187573200-187596600	Weak transcription	Esophagus	oesophagus
3	chr4:187574400-187591600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr4:187579600-187595400	Weak transcription	Brain Substantia Nigra	brain
5	chr4:187583000-187614400	Weak transcription	Colonic Mucosa	Colon
6	chr4:187583200-187591000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr4:187583400-187591000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:187587400-187591600	Genic enhancers	HSMM	muscle
9	chr4:187587400-187591600	Enhancers	HSMMtube	muscle
10	chr4:187587600-187591000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:187587600-187610200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr4:187587800-187597000	Weak transcription	Fetal Kidney	kidney
13	chr4:187588000-187594200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:187588400-187597800	Weak transcription	Stomach Mucosa	stomach
15	chr4:187588400-187604400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr4:187590000-187591000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr4:187590000-187591200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:187590000-187591200	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr4:187590200-187591000	Active TSS	Brain Anterior Caudate	brain
20	chr4:187590200-187591200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:187590200-187591200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr4:187590200-187591200	Enhancers	Fetal Heart	heart
23	chr4:187590200-187591200	Enhancers	Left Ventricle	heart
24	chr4:187590200-187591200	Enhancers	Pancreas	Pancrea
25	chr4:187590200-187591400	Enhancers	Muscle Satellite Cultured Cells	--
26	chr4:187590200-187591400	Enhancers	Stomach Smooth Muscle	stomach
27	chr4:187590200-187591400	Genic enhancers	NH-A	brain
28	chr4:187590200-187592000	Enhancers	Colon Smooth Muscle	Colon
29	chr4:187590200-187592200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr4:187590200-187592200	Genic enhancers	HMEC	breast
31	chr4:187590200-187592400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:187590200-187594200	Enhancers	Rectal Smooth Muscle	rectum
33	chr4:187590400-187591000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr4:187590400-187591000	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr4:187590400-187591200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr4:187590400-187591200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr4:187590400-187591200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr4:187590400-187591200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:187590400-187591200	Enhancers	Adipose Nuclei	Adipose
40	chr4:187590400-187591200	Enhancers	Placenta	Placenta
41	chr4:187590400-187591200	Enhancers	Ovary	ovary
42	chr4:187590400-187591200	Enhancers	Placenta Amnion	Placenta Amnion
43	chr4:187590400-187591400	Enhancers	Fetal Lung	lung
44	chr4:187590400-187591600	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr4:187590400-187592200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr4:187590400-187592400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr4:187590400-187592400	Genic enhancers	NHEK	skin
48	chr4:187590600-187591000	Enhancers	NHLF	lung
49	chr4:187590600-187591200	Active TSS	Right Atrium	heart
50	chr4:187590600-187591200	Flanking Active TSS	Osteobl	bone

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