Variant report

Variant	rs4672527
Chromosome Location	chr2:62729674-62729675
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	chr2:62724451..62726698-chr2:62729521..62731262,2	MCF-7	breast:
2	chr2:62723131..62724977-chr2:62729168..62731291,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10191324	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10191428	0.92[AFR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11125927	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11903221	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][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];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12622031	0.83[JPT][hapmap]
rs13035295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13388903	0.97[AFR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13389363	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13396048	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233979	0.84[CEU][hapmap]
rs4286259	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4405748	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4672528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57645001	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6757222	0.92[ASN][1000 genomes]
rs6757448	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs73934251	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73934252	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73934253	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7582882	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7604354	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv535766	chr2:62177655-62929746	Bivalent/Poised TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv916190	chr2:62233785-63006200	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv932487	chr2:62258290-63006200	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv2751	chr2:62691264-62737131	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4672527	TMEM17	cis	parietal	SCAN
rs4672527	CEP68	cis	cerebellum	SCAN
rs4672527	CCT4	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62705800-62732200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:62713400-62732400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:62714200-62732400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:62716600-62732200	Weak transcription	Brain Angular Gyrus	brain
5	chr2:62716600-62732400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr2:62716800-62732000	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:62717600-62732400	Weak transcription	Fetal Muscle Leg	muscle
8	chr2:62717600-62732600	Weak transcription	Ovary	ovary
9	chr2:62719600-62732800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:62723000-62732200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:62723600-62732200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:62725000-62732000	Weak transcription	Fetal Intestine Large	intestine
13	chr2:62725000-62732400	Weak transcription	Fetal Lung	lung
14	chr2:62725200-62732200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:62726400-62732400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:62726400-62732400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr2:62726800-62732200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:62727200-62732200	Weak transcription	Osteobl	bone
19	chr2:62727200-62732400	Weak transcription	HSMMtube	muscle
20	chr2:62728000-62729800	Enhancers	HepG2	liver
21	chr2:62728000-62732200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:62728200-62732600	Weak transcription	Left Ventricle	heart
23	chr2:62728400-62730000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:62728400-62732200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr2:62728600-62729800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:62728600-62729800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:62728600-62729800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:62728600-62731000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr2:62728800-62729800	Enhancers	A549	lung
30	chr2:62728800-62730000	Enhancers	K562	blood
31	chr2:62728800-62731000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr2:62728800-62731000	Enhancers	Pancreatic Islets	Pancreatic Islet
33	chr2:62728800-62732400	Weak transcription	Fetal Brain Female	brain
34	chr2:62728800-62732400	Weak transcription	Fetal Intestine Small	intestine
35	chr2:62729000-62732200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr2:62729000-62732400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr2:62729000-62732400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:62729200-62732200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:62729200-62732200	Weak transcription	NH-A	brain
40	chr2:62729200-62732400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:62729200-62732400	Weak transcription	Brain Anterior Caudate	brain
42	chr2:62729200-62732400	Weak transcription	HSMM	muscle
43	chr2:62729400-62732200	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr2:62729400-62732200	Weak transcription	NHLF	lung
45	chr2:62729400-62732400	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr2:62729600-62732000	Weak transcription	NHDF-Ad	bronchial
47	chr2:62729600-62732200	Weak transcription	NHEK	skin
48	chr2:62729600-62732400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:62729600-62732400	Weak transcription	Adipose Nuclei	Adipose
50	chr2:62729600-62732400	Weak transcription	HMEC	breast

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