Variant report

Variant	rs2526327
Chromosome Location	chr17:34256906-34256907
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 125 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs11080360	0.89[ASN][1000 genomes]
rs11080361	0.89[ASN][1000 genomes]
rs11080362	0.89[ASN][1000 genomes]
rs11650409	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11652536	0.87[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs11653016	0.89[ASN][1000 genomes]
rs11653051	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11653204	0.88[ASN][1000 genomes]
rs11654713	0.88[ASN][1000 genomes]
rs11655533	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11656556	0.88[ASN][1000 genomes]
rs11657908	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11868801	0.89[ASN][1000 genomes]
rs11869976	0.89[ASN][1000 genomes]
rs16971670	0.89[ASN][1000 genomes]
rs2107538	0.92[GIH][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs2107540	0.88[ASN][1000 genomes]
rs2251660	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2280787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2291299	0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs2376287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2526328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2702947	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2702948	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2735475	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28550999	0.89[ASN][1000 genomes]
rs28722787	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28739295	0.88[ASN][1000 genomes]
rs28912068	0.85[ASN][1000 genomes]
rs34369685	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3760447	0.85[ASN][1000 genomes]
rs3809769	0.87[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs3817655	0.82[EUR][1000 genomes]
rs3817656	0.82[ASN][1000 genomes]
rs3826404	0.89[TSI][hapmap]
rs4251751	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs4251752	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs4251791	0.80[EUR][1000 genomes]
rs4795089	0.80[CHB][hapmap];0.87[JPT][hapmap]
rs4795090	0.86[GIH][hapmap];0.96[TSI][hapmap]
rs4795095	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs4795099	0.84[ASN][1000 genomes]
rs4795100	0.89[ASN][1000 genomes]
rs4795101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4796105	0.88[TSI][hapmap]
rs4796107	0.80[CHB][hapmap];0.87[JPT][hapmap]
rs4796108	0.88[JPT][hapmap]
rs4796112	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs4796114	0.85[JPT][hapmap]
rs4796115	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs4796118	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs4796119	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs4796120	0.87[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs4796123	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs4796124	0.88[ASN][1000 genomes]
rs4796125	0.88[ASN][1000 genomes]
rs4796126	0.86[ASN][1000 genomes]
rs4796127	0.88[ASN][1000 genomes]
rs4796128	0.94[GIH][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs4796130	0.89[ASN][1000 genomes]
rs4796131	0.89[ASN][1000 genomes]
rs4796133	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4796134	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4796136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4796137	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4796138	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56294660	0.89[ASN][1000 genomes]
rs56344830	0.86[ASN][1000 genomes]
rs59338510	0.88[ASN][1000 genomes]
rs6505496	0.86[GIH][hapmap];0.96[TSI][hapmap]
rs7211393	0.86[EUR][1000 genomes]
rs7213636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7215845	0.88[EUR][1000 genomes]
rs8066406	0.89[EUR][1000 genomes]
rs9303691	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs9303693	0.89[ASN][1000 genomes]
rs9754	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9789051	0.88[ASN][1000 genomes]
rs9889274	0.80[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs9889977	0.89[ASN][1000 genomes]
rs9890583	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9891064	0.89[ASN][1000 genomes]
rs9893004	0.89[ASN][1000 genomes]
rs9894314	0.89[ASN][1000 genomes]
rs9894799	0.89[ASN][1000 genomes]
rs9896265	0.88[ASN][1000 genomes]
rs9896658	0.89[ASN][1000 genomes]
rs9897665	0.89[ASN][1000 genomes]
rs9898132	0.87[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs9898152	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs9899215	0.89[ASN][1000 genomes]
rs9899866	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9899870	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9899881	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9900236	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9901195	0.89[ASN][1000 genomes]
rs9901418	0.89[ASN][1000 genomes]
rs9903590	0.89[ASN][1000 genomes]
rs9904675	0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9907145	0.89[ASN][1000 genomes]
rs9907295	0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9908011	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9908525	0.89[ASN][1000 genomes]
rs9908907	0.82[ASN][1000 genomes]
rs9908928	0.81[EUR][1000 genomes]
rs9909050	0.87[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs9911016	0.89[ASN][1000 genomes]
rs9912049	0.89[ASN][1000 genomes]
rs9912284	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9912552	0.82[ASN][1000 genomes]
rs9912571	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9912793	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9912894	0.89[ASN][1000 genomes]
rs9913488	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9913559	1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9914401	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs9914468	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3380735	chr17:34246253-34271932	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1063100	chr17:34246253-34397598	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv833424	chr17:34246253-34419476	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1056950	chr17:34246253-34442620	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv1059795	chr17:34246253-34442620	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv1060457	chr17:34246253-34442620	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv543320	chr17:34246253-34442620	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv949160	chr17:34246253-34442620	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2526327	AMAC1	cis	cerebellum	SCAN
rs2526327	RDM1	cis	Lymphoblastoid	GTEx
rs2526327	RDM1	cis	lymphoblastoid	seeQTL
rs2526327	RDM1	cis	parietal	SCAN
rs2526327	C17orf50	cis	cerebellum	SCAN
rs2526327	NFS1	trans	multi-tissue	Pritchard

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:34244800-34257000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr17:34245600-34257200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:34247400-34257000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr17:34247600-34257000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr17:34249800-34257000	Weak transcription	Fetal Muscle Leg	muscle
6	chr17:34250200-34257000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr17:34250200-34257000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr17:34251400-34257000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr17:34251600-34257000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr17:34251800-34257000	Weak transcription	Primary B cells from cord blood	blood
11	chr17:34251800-34257000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr17:34251800-34257000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr17:34251800-34257000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr17:34252400-34257000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr17:34255200-34257000	Weak transcription	Liver	Liver
16	chr17:34255400-34257000	Weak transcription	Fetal Intestine Large	intestine
17	chr17:34255600-34257000	Weak transcription	Fetal Intestine Small	intestine
18	chr17:34256600-34257000	Enhancers	Brain Germinal Matrix	brain
19	chr17:34256600-34257000	Enhancers	HMEC	breast
20	chr17:34256600-34257200	Enhancers	Primary T cells fromperipheralblood	blood
21	chr17:34256600-34257200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr17:34256800-34257000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr17:34256800-34257000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
24	chr17:34256800-34257000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr17:34256800-34257000	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr17:34256800-34257000	Enhancers	Primary T cells from cord blood	blood
27	chr17:34256800-34257000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr17:34256800-34257000	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr17:34256800-34257000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr17:34256800-34257000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr17:34256800-34257000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr17:34256800-34257000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr17:34256800-34257000	Enhancers	Colonic Mucosa	Colon
34	chr17:34256800-34257000	Enhancers	Duodenum Mucosa	Duodenum
35	chr17:34256800-34257000	Enhancers	Fetal Stomach	stomach
36	chr17:34256800-34257000	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr17:34256800-34257000	Enhancers	A549	lung
38	chr17:34256800-34257000	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr17:34256800-34257000	Enhancers	NHEK	skin
40	chr17:34256800-34257000	Enhancers	Osteobl	bone
41	chr17:34256800-34257200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr17:34256800-34257200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr17:34256800-34257200	Enhancers	Primary hematopoietic stem cells	blood
44	chr17:34256800-34257200	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr17:34256800-34257200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr17:34256800-34257200	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr17:34256800-34257200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr17:34256800-34257200	Enhancers	Fetal Heart	heart
49	chr17:34256800-34257200	Enhancers	Fetal Lung	lung
50	chr17:34256800-34257200	Enhancers	Thymus	Thymus

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