Variant report

Variant	rs3749507
Chromosome Location	chr4:128565000-128565001
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:128553241..128556204-chr4:128562261..128565320,4	K562	blood:
2	chr4:128561660..128563498-chr4:128564714..128566263,2	MCF-7	breast:
3	chr4:128564328..128566993-chr4:128568354..128570269,2	MCF-7	breast:
4	chr4:128552418..128557041-chr4:128564673..128569925,6	K562	blood:

Variant related genes	Relation type
ENSG00000164066	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10023894	0.86[ASN][1000 genomes]
rs1018289	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs10857125	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11098931	0.89[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs11098933	0.92[CEU][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs1159021	0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[ASN][1000 genomes]
rs1159022	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11732886	0.80[CEU][hapmap]
rs11946559	0.90[ASN][1000 genomes]
rs12331481	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12509562	0.85[EUR][1000 genomes]
rs12639763	0.89[ASN][1000 genomes]
rs13126673	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13151291	0.85[CEU][hapmap]
rs1399210	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1399211	0.85[EUR][1000 genomes]
rs1459049	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1514298	0.89[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs1514299	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1913464	0.86[EUR][1000 genomes]
rs2048685	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2048686	0.84[EUR][1000 genomes]
rs2125573	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2255457	0.89[CEU][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs2279070	0.83[ASN][1000 genomes]
rs2391188	0.89[CEU][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs2391189	0.86[EUR][1000 genomes]
rs28656192	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34066758	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4340805	0.88[ASN][1000 genomes]
rs4543128	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4833380	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4833383	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4833384	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4833386	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4834206	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4834210	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4834211	0.89[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[ASN][1000 genomes]
rs4834214	0.85[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.82[ASN][1000 genomes]
rs6534630	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6534631	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs6534632	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];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6534633	0.85[CEU][hapmap]
rs6810904	0.83[EUR][1000 genomes]
rs6828511	0.81[CEU][hapmap]
rs6847056	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6847397	0.89[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs6854119	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6858855	0.81[CEU][hapmap]
rs7664217	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7678085	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.84[ASN][1000 genomes]
rs7679782	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7683627	0.81[CEU][hapmap]
rs7686395	0.89[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs7692114	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7694079	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs922060	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879915	chr4:128167093-129150590	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1029214	chr4:128292215-128683123	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537247	chr4:128292215-128683123	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv817326	chr4:128292216-128915201	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv879916	chr4:128422400-128694288	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv879917	chr4:128478408-128841252	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv830056	chr4:128517139-128676557	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv879918	chr4:128543742-128694288	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv879919	chr4:128543742-128697519	Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
10	nsv879920	chr4:128554404-128694288	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv879921	chr4:128554404-128766074	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
12	nsv879922	chr4:128554404-128901402	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
13	nsv879923	chr4:128554404-129068179	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3749507	PLK4	cis	cerebellum	SCAN
rs3749507	LARP1B	cis	parietal	SCAN
rs3749507	HSPA4L	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:128554600-128627400	Weak transcription	Pancreas	Pancrea
2	chr4:128554600-128644800	Weak transcription	Lung	lung
3	chr4:128554800-128565000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:128554800-128566200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:128554800-128596600	Weak transcription	Fetal Muscle Leg	muscle
6	chr4:128554800-128604400	Weak transcription	Right Ventricle	heart
7	chr4:128555000-128566200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr4:128555000-128566200	Weak transcription	Fetal Intestine Small	intestine
9	chr4:128555000-128566200	Weak transcription	Fetal Stomach	stomach
10	chr4:128555000-128568200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:128555000-128570000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr4:128555000-128579400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr4:128555000-128608800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:128555200-128565000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr4:128555200-128565000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr4:128555200-128569800	Weak transcription	Fetal Heart	heart
17	chr4:128555200-128577000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr4:128555200-128577000	Weak transcription	A549	lung
19	chr4:128555200-128577200	Weak transcription	HepG2	liver
20	chr4:128555200-128577400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:128555200-128578600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:128555200-128586000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr4:128555200-128587400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr4:128555400-128565000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr4:128555400-128567800	Weak transcription	NHEK	skin
26	chr4:128555600-128577200	Weak transcription	K562	blood
27	chr4:128555600-128627600	Weak transcription	Brain Angular Gyrus	brain
28	chr4:128555800-128565000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr4:128556200-128590200	Weak transcription	NH-A	brain
30	chr4:128556200-128615600	Weak transcription	Fetal Brain Male	brain
31	chr4:128557800-128567600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr4:128559400-128583000	Weak transcription	Liver	Liver
33	chr4:128559800-128565000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr4:128560400-128565000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr4:128562400-128582600	Weak transcription	Spleen	Spleen
36	chr4:128562800-128566200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr4:128562800-128578000	Weak transcription	Adipose Nuclei	Adipose
38	chr4:128562800-128581400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:128562800-128597400	Weak transcription	Esophagus	oesophagus
40	chr4:128562800-128616400	Weak transcription	Aorta	Aorta
41	chr4:128563000-128565000	Weak transcription	Brain Anterior Caudate	brain
42	chr4:128563000-128565000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr4:128563000-128566200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:128563000-128568000	Weak transcription	HSMMtube	muscle
45	chr4:128563000-128570200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr4:128563600-128614000	Weak transcription	Stomach Smooth Muscle	stomach
47	chr4:128563600-128627400	Weak transcription	Brain Substantia Nigra	brain
48	chr4:128564000-128565000	Weak transcription	Fetal Lung	lung
49	chr4:128564000-128566600	Weak transcription	NHDF-Ad	bronchial
50	chr4:128564000-128569200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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