Variant report

Variant	rs17239459
Chromosome Location	chr15:57539254-57539255
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs11071307	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11071310	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11636655	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12324235	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12593843	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12595074	0.81[GIH][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs17239222	0.95[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs17819940	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs17820018	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17820095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1867638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1870870	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2126402	0.95[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs2169468	0.95[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs2248620	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2252289	1.00[ASW][hapmap];0.90[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs2290939	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2431032	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2440972	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2440974	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2441924	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2464427	1.00[ASW][hapmap];0.90[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs2464428	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2470083	0.90[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2470084	0.90[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2470085	1.00[YRI][hapmap]
rs2591062	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2591066	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2593217	0.95[CEU][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs2593221	0.95[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2593223	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2593233	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2593234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2593236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2615228	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2703588	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2703599	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2703600	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2733187	1.00[ASW][hapmap];0.90[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs2733304	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2733309	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2733318	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2733320	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2733329	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2733330	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2920270	0.95[CEU][hapmap];1.00[YRI][hapmap]
rs2921430	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2951902	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2957578	1.00[ASW][hapmap];0.90[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs2957592	0.95[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs2962988	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2962994	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2962995	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap]
rs3794617	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4378569	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4774920	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56151428	0.81[EUR][1000 genomes]
rs6493909	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7165729	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7167268	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7180513	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7182038	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7182188	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72731958	0.82[AFR][1000 genomes]
rs72731964	0.94[AFR][1000 genomes]
rs72731970	0.82[AFR][1000 genomes]
rs72731974	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs72731986	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs734033	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8023315	1.00[YRI][hapmap]
rs8024830	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8027348	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8035097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8037987	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8042190	0.95[CEU][hapmap]
rs8042322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8043103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs935323	1.00[YRI][hapmap]
rs935328	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv457164	chr15:57495060-57559387	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv569578	chr15:57495060-57559387	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv833021	chr15:57495413-57751366	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv974581	chr15:57538491-57540100	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17239459	GCOM1	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57511800-57551600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:57511800-57565000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:57519600-57544600	Weak transcription	Psoas Muscle	Psoas
4	chr15:57520400-57576000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr15:57520800-57544600	Weak transcription	Colon Smooth Muscle	Colon
6	chr15:57522400-57565400	Weak transcription	Spleen	Spleen
7	chr15:57522800-57585000	Strong transcription	Fetal Thymus	thymus
8	chr15:57524400-57540600	Strong transcription	Primary T cells from cord blood	blood
9	chr15:57525600-57556800	Weak transcription	Pancreas	Pancrea
10	chr15:57526000-57542600	Weak transcription	Right Ventricle	heart
11	chr15:57526000-57550200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:57526600-57545400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr15:57526600-57554400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr15:57526600-57574200	Weak transcription	Hela-S3	cervix
15	chr15:57526800-57545400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr15:57526800-57554200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr15:57528200-57545200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr15:57528400-57545400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr15:57528400-57554800	Weak transcription	NHEK	skin
20	chr15:57529000-57545400	Weak transcription	HMEC	breast
21	chr15:57529400-57543400	Weak transcription	HUVEC	blood vessel
22	chr15:57529600-57540000	Weak transcription	Fetal Heart	heart
23	chr15:57530200-57543400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr15:57530800-57551200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:57531000-57542400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:57531400-57541200	Strong transcription	Fetal Muscle Trunk	muscle
27	chr15:57531600-57540200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:57533600-57568800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr15:57535000-57539600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr15:57535000-57540000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr15:57535000-57541200	Strong transcription	NH-A	brain
32	chr15:57535200-57540000	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr15:57535200-57542600	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr15:57535400-57540000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr15:57535400-57540000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr15:57535600-57539600	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr15:57535600-57539600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr15:57535600-57539800	Strong transcription	Adipose Nuclei	Adipose
39	chr15:57535600-57540200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr15:57535600-57540200	Strong transcription	Primary B cells from peripheral blood	blood
41	chr15:57535600-57540200	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr15:57535600-57540400	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr15:57535600-57540400	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr15:57535600-57540600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr15:57535600-57541400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:57535600-57541800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr15:57535800-57540000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr15:57535800-57540400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr15:57536000-57540600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr15:57536000-57540600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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