Variant report

Variant	rs7636249
Chromosome Location	chr3:134043422-134043423
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: 5 )

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	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][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[CHD][hapmap];1.00[ASN][1000 genomes]
rs11923513	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11928672	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11928742	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][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	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13084853	1.00[CHB][hapmap];1.00[CHD][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[CHD][hapmap];1.00[ASN][1000 genomes]
rs17312996	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs17313003	1.00[CHB][hapmap];1.00[CHD][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	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][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	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]
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	0.82[CEU][hapmap];1.00[YRI][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]
rs7637889	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs7638751	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642519	0.89[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7647682	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[TSI][hapmap]
rs7647778	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]
rs7651578	1.00[ASN][1000 genomes]
rs9826364	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7636249	CCRL1	cis	cerebellum	SCAN
rs7636249	PPP2R3A	cis	cerebellum	SCAN
rs7636249	TMEM22	cis	parietal	SCAN
rs7636249	CEP70	cis	cerebellum	SCAN
rs7636249	FAIM	cis	parietal	SCAN

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	chr3:134039800-134044000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:134039800-134044200	Weak transcription	Hela-S3	cervix
12	chr3:134039800-134045000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:134039800-134045600	Enhancers	NHEK	skin
14	chr3:134040000-134044000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:134040000-134044600	Weak transcription	NH-A	brain
16	chr3:134040000-134044800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr3:134041200-134046000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:134041200-134056600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr3:134041600-134044400	Enhancers	A549	lung
20	chr3:134041600-134047400	Enhancers	Pancreas	Pancrea
21	chr3:134041800-134044800	Weak transcription	Psoas Muscle	Psoas
22	chr3:134042000-134060800	Enhancers	Placenta	Placenta
23	chr3:134042200-134043600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:134042200-134050600	Enhancers	Placenta Amnion	Placenta Amnion
25	chr3:134042200-134052400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:134042600-134045000	Enhancers	Adipose Nuclei	Adipose
27	chr3:134042600-134046000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:134042600-134046600	Enhancers	Spleen	Spleen
29	chr3:134042600-134054000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:134042600-134054400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:134042800-134045600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:134042800-134046000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:134042800-134046000	Enhancers	Osteobl	bone
34	chr3:134042800-134057000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:134043000-134046200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:134043200-134044200	Weak transcription	HepG2	liver
37	chr3:134043200-134045400	Enhancers	Gastric	stomach
38	chr3:134043200-134046000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:134043200-134046000	Enhancers	NHDF-Ad	bronchial
40	chr3:134043200-134046200	Enhancers	NHLF	lung
41	chr3:134043200-134046800	Enhancers	Lung	lung
42	chr3:134043200-134047600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr3:134043400-134044600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr3:134043400-134046000	Enhancers	Muscle Satellite Cultured Cells	--
45	chr3:134043400-134046000	Enhancers	HMEC	breast
46	chr3:134043400-134046000	Enhancers	HSMM	muscle
47	chr3:134043400-134046200	Enhancers	HSMMtube	muscle

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