Variant report

Variant	rs17623445
Chromosome Location	chr4:165894658-165894659
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10007789	0.84[CHD][hapmap]
rs10517825	0.84[CHD][hapmap]
rs11100583	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11942693	0.90[CHB][hapmap];0.95[GIH][hapmap];0.96[TSI][hapmap]
rs11942750	0.90[CHB][hapmap]
rs12507869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs12510464	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12512234	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12647427	0.84[CEU][hapmap];0.89[CHB][hapmap]
rs13110309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13110766	0.85[TSI][hapmap]
rs13111010	0.81[TSI][hapmap]
rs13120990	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs13134940	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];0.95[MKK][hapmap];0.96[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]
rs13137799	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs13140290	0.81[ASN][1000 genomes]
rs13144590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13151290	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13151735	0.84[CHB][hapmap]
rs1401399	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1401400	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1401401	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2280325	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3733418	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3733419	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3889248	0.91[CHD][hapmap];0.80[JPT][hapmap]
rs4234889	0.84[ASN][1000 genomes]
rs4395461	0.84[ASN][1000 genomes]
rs4690797	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4691138	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4691139	0.80[CHD][hapmap]
rs4691141	0.81[JPT][hapmap]
rs61641856	0.84[ASN][1000 genomes]
rs6834073	0.86[CHD][hapmap];0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs71641138	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72697952	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7656863	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7657444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7657639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7693977	0.80[CHD][hapmap]
rs8180162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs869867	0.84[CEU][hapmap]
rs9762579	0.82[CHD][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	nsv1019150	chr4:165505585-165907924	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1026152	chr4:165622244-166027447	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv537336	chr4:165622244-166027447	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1022210	chr4:165792630-166251612	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv537337	chr4:165792630-166251612	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv880382	chr4:165793001-165964290	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	esv2757965	chr4:165801816-165976350	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	esv2759299	chr4:165801816-165976350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv528686	chr4:165814359-165930168	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv1015970	chr4:165852926-165973078	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1021905	chr4:165852926-166212878	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
12	nsv830140	chr4:165855999-165956612	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv533191	chr4:165879671-166171638	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17623445	C4orf39	cis	parietal	SCAN
rs17623445	C4orf39	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:165878800-165895000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:165878800-165895200	Weak transcription	Fetal Thymus	thymus
3	chr4:165878800-165897800	Weak transcription	Left Ventricle	heart
4	chr4:165878800-165898200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:165879000-165897600	Weak transcription	Fetal Lung	lung
6	chr4:165879000-165897800	Weak transcription	Adipose Nuclei	Adipose
7	chr4:165879200-165894800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr4:165879400-165897600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:165879400-165898000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:165879800-165898000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:165880000-165897600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:165880200-165897600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr4:165881400-165897800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:165881600-165897600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:165881600-165898000	Weak transcription	Osteobl	bone
16	chr4:165882200-165897800	Weak transcription	HSMM	muscle
17	chr4:165884600-165898200	Weak transcription	Ovary	ovary
18	chr4:165886800-165897600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr4:165887000-165898200	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr4:165887200-165898000	Weak transcription	Primary B cells from cord blood	blood
21	chr4:165888800-165895600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:165888800-165895600	Weak transcription	GM12878-XiMat	blood
23	chr4:165888800-165897600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr4:165888800-165898000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:165889200-165895200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr4:165889400-165897800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:165889800-165897800	Weak transcription	Right Ventricle	heart
28	chr4:165891000-165896200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:165891400-165897600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:165891400-165897800	Weak transcription	Brain Substantia Nigra	brain
31	chr4:165891800-165896400	Strong transcription	Fetal Muscle Leg	muscle
32	chr4:165892000-165895600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr4:165892000-165895800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:165892000-165896000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:165892000-165896000	Strong transcription	Fetal Intestine Small	intestine
36	chr4:165892000-165896600	Strong transcription	Fetal Stomach	stomach
37	chr4:165892200-165897600	Weak transcription	NHDF-Ad	bronchial
38	chr4:165892200-165898200	Weak transcription	Lung	lung
39	chr4:165892400-165896000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr4:165892800-165897600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr4:165893400-165895400	Strong transcription	Primary B cells from peripheral blood	blood
42	chr4:165893400-165896000	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr4:165893400-165896200	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr4:165893400-165896600	Strong transcription	Fetal Intestine Large	intestine
45	chr4:165893600-165896000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr4:165894000-165898000	Weak transcription	Fetal Brain Female	brain
47	chr4:165894200-165895000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr4:165894400-165898400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr4:165894600-165895600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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