Variant report

Variant	rs9521825
Chromosome Location	chr13:111193558-111193559
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:111192777..111195379-chr13:111196356..111198456,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs2148079	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2148080	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2391835	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2391836	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2391838	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2391839	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2391840	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2391841	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2477910	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2477911	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2479431	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2479434	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331596	0.83[CEU][hapmap];0.89[MEX][hapmap];0.87[EUR][1000 genomes]
rs34890574	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35691072	0.86[ASN][1000 genomes]
rs377380	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs394559	0.88[ASN][1000 genomes]
rs4267185	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4268628	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4393429	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4448791	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6492282	0.88[ASN][1000 genomes]
rs7140104	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7339017	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7339377	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9515251	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9515252	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9521823	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9521824	0.94[CEU][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9521826	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9521836	1.00[MEX][hapmap];0.80[EUR][1000 genomes]
rs9559839	0.88[ASN][1000 genomes]
rs9588184	0.92[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][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	nsv1046423	chr13:110936104-111286607	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv832720	chr13:111100235-111295993	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1046291	chr13:111125747-111257861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1045143	chr13:111126822-111242791	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1044234	chr13:111143053-111370580	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	216 gene(s)	inside rSNPs	diseases
6	nsv949634	chr13:111151460-111582996	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
7	nsv901010	chr13:111165390-111286592	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv1053922	chr13:111167764-111330876	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1043849	chr13:111167764-111340418	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv541924	chr13:111167764-111340418	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer 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	25 gene(s)	inside rSNPs	diseases
11	nsv1036160	chr13:111167764-111347308	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	nsv541925	chr13:111167764-111347308	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer 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	25 gene(s)	inside rSNPs	diseases
13	nsv901011	chr13:111168951-111280002	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
14	nsv977187	chr13:111192304-111193719	Weak transcription Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9521825	ARHGEF7	cis	parietal	SCAN
rs9521825	RAB20	cis	Thyroid	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111160800-111209600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr13:111182400-111193800	Weak transcription	HepG2	liver
3	chr13:111182400-111203600	Weak transcription	Brain Substantia Nigra	brain
4	chr13:111184000-111199600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr13:111184000-111211800	Weak transcription	HMEC	breast
6	chr13:111184200-111196400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr13:111184200-111197000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr13:111184600-111209800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr13:111185800-111193600	Weak transcription	Colon Smooth Muscle	Colon
10	chr13:111188200-111194000	Weak transcription	Brain Hippocampus Middle	brain
11	chr13:111188400-111196400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr13:111188400-111203600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr13:111189000-111193800	Weak transcription	Fetal Intestine Large	intestine
14	chr13:111189000-111198600	Weak transcription	NHLF	lung
15	chr13:111189000-111198800	Weak transcription	Small Intestine	intestine
16	chr13:111189000-111201600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr13:111190000-111193800	Weak transcription	K562	blood
18	chr13:111190400-111199400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr13:111191200-111213000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr13:111191400-111193600	Weak transcription	Osteobl	bone
21	chr13:111191400-111193800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr13:111191400-111193800	Weak transcription	Fetal Kidney	kidney
23	chr13:111191400-111194000	Weak transcription	Lung	lung
24	chr13:111191400-111194200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr13:111191400-111199400	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr13:111191400-111199400	Weak transcription	HSMM	muscle
27	chr13:111191400-111203600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr13:111191400-111207200	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr13:111191800-111194600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr13:111191800-111199000	Weak transcription	Colonic Mucosa	Colon
31	chr13:111192200-111195400	Enhancers	Fetal Heart	heart
32	chr13:111192200-111212000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr13:111193000-111195000	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr13:111193000-111195200	Enhancers	Placenta Amnion	Placenta Amnion
35	chr13:111193200-111193600	Enhancers	Adipose Nuclei	Adipose
36	chr13:111193200-111193600	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr13:111193200-111194200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr13:111193200-111194200	Enhancers	Placenta	Placenta
39	chr13:111193200-111194400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr13:111193200-111194400	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr13:111193200-111194400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr13:111193200-111194400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr13:111193200-111194400	Enhancers	Fetal Stomach	stomach
44	chr13:111193200-111194400	Enhancers	Right Atrium	heart
45	chr13:111193200-111194600	Enhancers	Right Ventricle	heart
46	chr13:111193200-111194800	Enhancers	Duodenum Mucosa	Duodenum
47	chr13:111193200-111194800	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr13:111193200-111195000	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr13:111193200-111195000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr13:111193200-111195200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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