Variant report

Variant	rs11729044
Chromosome Location	chr4:86049045-86049046
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	chr4:86048857..86049411-chr4:86239183..86239916,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10516739	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap]
rs12502228	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap]
rs13130662	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap]
rs17009660	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap]
rs17009674	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap]
rs2869283	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs4639062	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap]
rs56094513	0.84[ASN][1000 genomes]
rs60956803	0.84[ASN][1000 genomes]
rs6531790	0.87[ASN][1000 genomes]
rs6850004	0.88[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	esv1829655	chr4:85577491-86292692	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv519588	chr4:85762385-86591202	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	esv3367963	chr4:85911017-86246036	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv461566	chr4:85988032-86725502	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv594747	chr4:85988032-86725502	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
6	nsv470048	chr4:85998783-86720838	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
7	nsv427685	chr4:86032872-86340548	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11729044	MAPK10	cis	cerebellum	SCAN
rs11729044	MRPS18C	cis	cerebellum	SCAN
rs11729044	NCRNA00247	cis	cerebellum	SCAN
rs11729044	ARHGAP24	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86046600-86049400	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr4:86046800-86051000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr4:86047000-86049200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:86047600-86049200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:86047600-86049200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr4:86047800-86049400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:86048000-86049400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr4:86048000-86051400	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr4:86048200-86050000	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr4:86048400-86049200	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr4:86048400-86050200	Enhancers	H1 Cell Line	embryonic stem cell
12	chr4:86048400-86051400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr4:86048600-86049200	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr4:86048600-86049800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr4:86048600-86049800	Enhancers	Fetal Muscle Leg	muscle
16	chr4:86048800-86049200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr4:86048800-86049200	Enhancers	Brain Germinal Matrix	brain
18	chr4:86048800-86049200	Enhancers	Fetal Brain Female	brain
19	chr4:86048800-86049200	Enhancers	Fetal Muscle Trunk	muscle
20	chr4:86048800-86049400	Enhancers	Adipose Nuclei	Adipose
21	chr4:86048800-86049400	Enhancers	Placenta	Placenta
22	chr4:86048800-86049800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr4:86048800-86050000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:86049000-86049400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr4:86049000-86049400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr4:86049000-86049400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr4:86049000-86049400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:86049000-86049400	Enhancers	Brain Hippocampus Middle	brain
29	chr4:86049000-86049400	Enhancers	Gastric	stomach
30	chr4:86049000-86049400	Enhancers	Pancreas	Pancrea
31	chr4:86049000-86049600	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr4:86049000-86051600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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