Variant report

Variant	rs7647778
Chromosome Location	chr3:134043264-134043265
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	chr3:134025978..134037323-chr3:134040972..134053086,34	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AMOTL2-2	chr3:134042592-134045369	XLOC_003261

Variant related genes	Relation type
ENSG00000240006	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10935116	1.00[CHB][hapmap]
rs11707704	1.00[ASN][1000 genomes]
rs11917363	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919447	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11923513	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11928672	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11928742	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs11928907	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487438	1.00[CHB][hapmap]
rs13069766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13071132	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13084853	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13085145	0.95[EUR][1000 genomes]
rs13090504	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097926	0.94[EUR][1000 genomes]
rs1498730	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17312996	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17313003	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs34006849	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34524468	1.00[ASN][1000 genomes]
rs34549392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35098409	1.00[ASN][1000 genomes]
rs35471660	1.00[ASN][1000 genomes]
rs35527623	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35558600	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35878592	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846052	1.00[ASN][1000 genomes]
rs3913262	1.00[ASN][1000 genomes]
rs4234421	0.81[EUR][1000 genomes]
rs4339087	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs5002434	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5002435	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5002436	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5002437	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55682444	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56019901	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59458665	1.00[ASN][1000 genomes]
rs61145443	1.00[ASN][1000 genomes]
rs62271221	1.00[ASN][1000 genomes]
rs6439474	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6439476	1.00[ASN][1000 genomes]
rs6768709	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6772791	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776727	1.00[ASN][1000 genomes]
rs6804439	1.00[ASN][1000 genomes]
rs6809909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71331753	0.95[EUR][1000 genomes]
rs71331755	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72986454	1.00[ASN][1000 genomes]
rs73215399	1.00[ASN][1000 genomes]
rs7609766	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7613323	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7613440	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7613450	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7614069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636249	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637889	1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs7638751	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642519	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7647682	1.00[CHB][hapmap]
rs7651578	1.00[ASN][1000 genomes]
rs9826364	1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs9827007	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134034600-134046200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:134034800-134044200	Weak transcription	Right Ventricle	heart
3	chr3:134035000-134044000	Weak transcription	Fetal Heart	heart
4	chr3:134035000-134044200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:134035000-134045000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:134035000-134058800	Weak transcription	Liver	Liver
7	chr3:134036600-134044200	Weak transcription	Esophagus	oesophagus
8	chr3:134036600-134045000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:134036600-134050600	Weak transcription	Fetal Brain Female	brain
10	chr3:134037200-134043400	Weak transcription	HSMMtube	muscle
11	chr3:134039800-134044000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:134039800-134044200	Weak transcription	Hela-S3	cervix
13	chr3:134039800-134045000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:134039800-134045600	Enhancers	NHEK	skin
15	chr3:134040000-134043400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:134040000-134044000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:134040000-134044600	Weak transcription	NH-A	brain
18	chr3:134040000-134044800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:134040200-134043400	Weak transcription	HSMM	muscle
20	chr3:134041200-134046000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:134041200-134056600	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr3:134041600-134044400	Enhancers	A549	lung
23	chr3:134041600-134047400	Enhancers	Pancreas	Pancrea
24	chr3:134041800-134044800	Weak transcription	Psoas Muscle	Psoas
25	chr3:134042000-134060800	Enhancers	Placenta	Placenta
26	chr3:134042200-134043400	Weak transcription	HMEC	breast
27	chr3:134042200-134043600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:134042200-134050600	Enhancers	Placenta Amnion	Placenta Amnion
29	chr3:134042200-134052400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:134042600-134045000	Enhancers	Adipose Nuclei	Adipose
31	chr3:134042600-134046000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:134042600-134046600	Enhancers	Spleen	Spleen
33	chr3:134042600-134054000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:134042600-134054400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:134042800-134043400	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr3:134042800-134045600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:134042800-134046000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:134042800-134046000	Enhancers	Osteobl	bone
39	chr3:134042800-134057000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:134043000-134046200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:134043200-134044200	Weak transcription	HepG2	liver
42	chr3:134043200-134045400	Enhancers	Gastric	stomach
43	chr3:134043200-134046000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:134043200-134046000	Enhancers	NHDF-Ad	bronchial
45	chr3:134043200-134046200	Enhancers	NHLF	lung
46	chr3:134043200-134046800	Enhancers	Lung	lung
47	chr3:134043200-134047600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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