Variant report

Variant	rs3896424
Chromosome Location	chr9:72009528-72009529
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	chr9:72008297..72012521-chr9:72012809..72015808,4	MCF-7	breast:
2	chr9:71999516..72001197-chr9:72009030..72011371,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-APBA1-2	chr9:72009222-72010989	XLOC_007725

Variant related genes	Relation type
ENSG00000135063	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10116389	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10746613	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780334	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10780344	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11138491	0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1334312	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1761290	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1812971	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1929896	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2244720	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2309431	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2777866	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2777878	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2781521	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2781522	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2781527	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2781529	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35625426	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3934600	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4237232	0.87[ASN][1000 genomes]
rs4237233	0.87[AFR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4237234	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4483220	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4484762	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4503164	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4744894	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62570234	0.82[ASN][1000 genomes]
rs62570235	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs62570236	0.82[ASN][1000 genomes]
rs62570237	0.82[ASN][1000 genomes]
rs6559498	0.82[AFR][1000 genomes]
rs6559512	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6559513	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6559525	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6559527	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7856778	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7866250	0.82[AFR][1000 genomes]
rs9314682	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
7	nsv1035633	chr9:71995963-72176984	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv893431	chr9:72003036-72048098	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv8522	chr9:72009272-72034735	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71991800-72012200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:71992000-72009800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr9:71995000-72012600	Weak transcription	Aorta	Aorta
4	chr9:71997400-72009800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:72002800-72012400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:72003400-72010000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr9:72003400-72012400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:72003400-72012400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr9:72003600-72026200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr9:72006200-72013400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr9:72006400-72010000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr9:72006400-72010000	Enhancers	Right Ventricle	heart
13	chr9:72006400-72010400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr9:72006800-72010600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr9:72007000-72012800	Weak transcription	Esophagus	oesophagus
16	chr9:72007200-72010600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:72007400-72010600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr9:72007400-72012200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:72007600-72010400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr9:72007600-72012200	Weak transcription	Adipose Nuclei	Adipose
21	chr9:72007600-72026800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr9:72007800-72009800	Weak transcription	Brain Substantia Nigra	brain
23	chr9:72007800-72011800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr9:72007800-72012400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr9:72008000-72009800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr9:72008000-72012600	Weak transcription	HSMMtube	muscle
27	chr9:72008200-72009600	Weak transcription	Brain Anterior Caudate	brain
28	chr9:72008200-72010400	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr9:72008200-72012000	Weak transcription	Colon Smooth Muscle	Colon
30	chr9:72008200-72012400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr9:72008400-72010000	Weak transcription	Brain Angular Gyrus	brain
32	chr9:72008400-72010400	Weak transcription	Gastric	stomach
33	chr9:72008400-72012400	Weak transcription	Fetal Muscle Leg	muscle
34	chr9:72008400-72012400	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr9:72008600-72010400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr9:72008600-72012600	Weak transcription	Ovary	ovary
37	chr9:72008800-72010400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr9:72009000-72009600	Enhancers	Fetal Heart	heart
39	chr9:72009000-72011800	Weak transcription	Psoas Muscle	Psoas
40	chr9:72009000-72011800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr9:72009000-72012000	Weak transcription	Left Ventricle	heart
42	chr9:72009000-72012000	Weak transcription	Right Atrium	heart
43	chr9:72009000-72024400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr9:72009400-72011200	Strong transcription	Fetal Stomach	stomach
45	chr9:72009400-72013200	Enhancers	Brain Hippocampus Middle	brain

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