Variant report

Variant	rs3892193
Chromosome Location	chr9:71994002-71994003
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71991902..71994131-chr9:72003113..72004905,2	MCF-7	breast:
2	chr9:71992876..71994758-chr9:72000665..72002258,2	MCF-7	breast:
3	chr9:71649254..71651788-chr9:71993811..71996699,2	MCF-7	breast:
4	chr9:71940098..71942516-chr9:71992469..71994657,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135063	Chromatin interaction
ENSG00000165060	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10115490	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10118562	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10746595	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[ASN][1000 genomes]
rs10746596	0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10780321	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10780324	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10780326	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10780336	0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10867426	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10867436	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11138402	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11138412	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1334311	0.85[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3829094	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4112222	0.82[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs4255205	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4421413	0.82[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs4458929	0.97[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4492445	0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6559495	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7047788	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7870082	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv831610	chr9:71846941-72016835	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv893428	chr9:71926658-72027641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv893429	chr9:71961923-72047337	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv893430	chr9:71968730-72036369	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1047593	chr9:71971536-72180583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71962200-71994200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr9:71979000-72001800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:71983400-72001800	Weak transcription	Brain Anterior Caudate	brain
4	chr9:71985400-71994200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr9:71985400-72006600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr9:71986600-72002600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:71986800-71994200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr9:71988800-71998600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr9:71989000-72002800	Weak transcription	Brain Substantia Nigra	brain
10	chr9:71989600-71997000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr9:71990600-72000200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr9:71991200-71994200	Enhancers	HSMM	muscle
13	chr9:71991800-71994200	Weak transcription	Stomach Mucosa	stomach
14	chr9:71991800-72012200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr9:71992000-71994200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:71992000-71994200	Weak transcription	Aorta	Aorta
17	chr9:71992000-71994400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr9:71992000-71994400	Weak transcription	Pancreas	Pancrea
19	chr9:71992000-71994400	Weak transcription	NHLF	lung
20	chr9:71992000-71995800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:71992000-72001800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr9:71992000-72009800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr9:71992200-71997000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr9:71992200-72001800	Weak transcription	Adipose Nuclei	Adipose
25	chr9:71992400-71999400	Weak transcription	Brain Angular Gyrus	brain
26	chr9:71992400-72001800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr9:71992600-71994200	Weak transcription	Colon Smooth Muscle	Colon
28	chr9:71992600-71994200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr9:71992600-71994200	Weak transcription	Left Ventricle	heart
30	chr9:71992600-71994200	Weak transcription	Lung	lung
31	chr9:71992600-71994200	Weak transcription	NHDF-Ad	bronchial
32	chr9:71992600-71994400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr9:71992600-71995200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr9:71992600-71996000	Weak transcription	Right Atrium	heart
35	chr9:71992600-72000800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr9:71992600-72006200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr9:71992600-72006600	Weak transcription	Esophagus	oesophagus
38	chr9:71992800-71994200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr9:71992800-71994200	Weak transcription	Right Ventricle	heart
40	chr9:71992800-71994200	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr9:71992800-71997200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr9:71992800-71997400	Enhancers	Fetal Muscle Leg	muscle
43	chr9:71992800-71998200	Weak transcription	Ovary	ovary
44	chr9:71992800-71998400	Weak transcription	Fetal Stomach	stomach
45	chr9:71992800-72000200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr9:71992800-72001400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr9:71993000-71997000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr9:71993000-72006600	Weak transcription	Brain Hippocampus Middle	brain
49	chr9:71993200-71994200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr9:71993600-71994200	Weak transcription	Psoas Muscle	Psoas

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