Variant report

Variant	rs1034238
Chromosome Location	chr9:71986316-71986317
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr9:71986219-71986407	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
FAM189A2	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11139245	0.81[JPT][hapmap]
rs11139246	0.81[JPT][hapmap]
rs12551899	0.81[CEU][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap]
rs13284677	0.81[ASN][1000 genomes]
rs13285975	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13290847	0.80[JPT][hapmap]
rs13290881	0.85[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs13291679	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs13296504	0.82[JPT][hapmap]
rs13297121	0.92[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs13300133	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1475641	0.80[JPT][hapmap]
rs17412941	0.85[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap]
rs1855529	0.85[CEU][hapmap];0.80[CHB][hapmap];0.91[JPT][hapmap]
rs34133536	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34672585	0.81[ASN][1000 genomes]
rs4307408	0.89[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4351475	0.89[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4554547	0.81[ASN][1000 genomes]
rs4744884	0.87[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap]
rs4744885	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs4744893	0.92[CEU][hapmap];0.80[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60284429	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7028920	0.82[JPT][hapmap]
rs7853058	0.84[CEU][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap]
rs7855000	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7867609	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs867365	0.89[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs867366	0.89[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[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	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71962200-71994200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr9:71963200-71991800	Weak transcription	Pancreas	Pancrea
3	chr9:71972600-71991800	Weak transcription	Right Atrium	heart
4	chr9:71972800-71991400	Weak transcription	Fetal Muscle Leg	muscle
5	chr9:71977400-71992400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:71978800-71987200	Weak transcription	Psoas Muscle	Psoas
7	chr9:71978800-71989200	Weak transcription	Right Ventricle	heart
8	chr9:71978800-71991600	Weak transcription	Left Ventricle	heart
9	chr9:71979000-72001800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:71982200-71986400	Weak transcription	Ovary	ovary
11	chr9:71983400-72001800	Weak transcription	Brain Anterior Caudate	brain
12	chr9:71984600-71987000	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr9:71984800-71986600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr9:71985000-71987000	Enhancers	HUVEC	blood vessel
15	chr9:71985200-71986600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr9:71985200-71986800	Enhancers	HMEC	breast
17	chr9:71985200-71986800	Enhancers	NH-A	brain
18	chr9:71985400-71986800	Enhancers	Osteobl	bone
19	chr9:71985400-71994200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr9:71985400-72006600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr9:71985600-71986600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:71985600-71989600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr9:71985600-71991000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr9:71985600-71991200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr9:71985600-71991400	Weak transcription	Colon Smooth Muscle	Colon
26	chr9:71985600-71992400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr9:71985800-71986800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr9:71985800-71988600	Weak transcription	Fetal Heart	heart
29	chr9:71985800-71990200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr9:71986000-71986400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr9:71986000-71986600	Enhancers	Muscle Satellite Cultured Cells	--
32	chr9:71986000-71990800	Weak transcription	HSMMtube	muscle
33	chr9:71986200-71986600	Enhancers	Stomach Mucosa	stomach
34	chr9:71986200-71986800	Enhancers	H9 Cell Line	embryonic stem cell
35	chr9:71986200-71986800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr9:71986200-71990600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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