Variant report

Variant	rs13119941
Chromosome Location	chr4:8100158-8100159
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	chr4:8098463..8100832-chr4:8106304..8108910,3	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10008298	0.88[EUR][1000 genomes]
rs10938688	0.82[EUR][1000 genomes]
rs12501747	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12504271	0.89[EUR][1000 genomes]
rs12505302	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13103330	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1316347	0.85[EUR][1000 genomes]
rs1316348	0.83[EUR][1000 genomes]
rs28420077	0.86[EUR][1000 genomes]
rs28651106	0.86[EUR][1000 genomes]
rs34067387	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35735901	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4696751	0.89[EUR][1000 genomes]
rs4696752	0.89[EUR][1000 genomes]
rs4696753	0.88[EUR][1000 genomes]
rs4696754	0.87[EUR][1000 genomes]
rs62289380	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6849594	0.89[EUR][1000 genomes]
rs7661393	0.90[EUR][1000 genomes]
rs7669966	0.89[EUR][1000 genomes]
rs7674462	0.89[EUR][1000 genomes]
rs7674677	0.89[EUR][1000 genomes]
rs7675402	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	nsv469779	chr4:7965253-8177646	Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv482448	chr4:7965253-8177646	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
5	nsv829852	chr4:7991906-8151267	Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
6	nsv878581	chr4:8021592-8100272	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv878585	chr4:8023484-8116202	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv878586	chr4:8023484-8148159	Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv878591	chr4:8063501-8207083	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv461214	chr4:8085174-8119937	Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv593625	chr4:8085174-8119937	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv461215	chr4:8089598-8118561	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv1010809	chr4:8097627-8292324	Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
14	esv3407862	chr4:8097702-8100200	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13119941	GRPEL1	cis	parietal	SCAN
rs13119941	MRFAP1L1	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8081600-8114400	Weak transcription	Gastric	stomach
2	chr4:8082400-8102600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr4:8082400-8102800	Weak transcription	Right Atrium	heart
4	chr4:8084000-8104400	Weak transcription	Pancreas	Pancrea
5	chr4:8085800-8112000	Weak transcription	Brain Angular Gyrus	brain
6	chr4:8090400-8100600	Weak transcription	Left Ventricle	heart
7	chr4:8092000-8100400	Weak transcription	Right Ventricle	heart
8	chr4:8092800-8100800	Weak transcription	Hela-S3	cervix
9	chr4:8096800-8111600	Weak transcription	Brain Hippocampus Middle	brain
10	chr4:8097600-8101000	Weak transcription	Colon Smooth Muscle	Colon
11	chr4:8097800-8100600	Strong transcription	Esophagus	oesophagus
12	chr4:8097800-8105200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:8098400-8100200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr4:8098400-8109600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr4:8098400-8110200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr4:8098600-8103400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:8098800-8101200	Enhancers	Spleen	Spleen
18	chr4:8098800-8102600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:8099000-8104600	Weak transcription	Aorta	Aorta
20	chr4:8099400-8101200	Enhancers	Psoas Muscle	Psoas
21	chr4:8099400-8104000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:8099400-8105200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr4:8099800-8100400	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr4:8100000-8100200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr4:8100000-8101200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
26	chr4:8100000-8101600	Weak transcription	Adipose Nuclei	Adipose

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