Variant report

Variant	rs17526787
Chromosome Location	chr14:35230906-35230907
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10136352	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs10145299	0.92[ASN][1000 genomes]
rs10147130	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10147134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10150083	0.93[CHB][hapmap];0.94[JPT][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10150856	0.83[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11847610	0.87[EUR][1000 genomes]
rs1200414	0.90[JPT][hapmap]
rs12431818	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs12433706	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12435778	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs12435859	1.00[ASN][1000 genomes]
rs12587021	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs12587390	0.84[EUR][1000 genomes]
rs12590112	0.84[CEU][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs13379337	0.92[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.92[LWK][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17102726	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs17102768	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs17102795	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs17102829	1.00[JPT][hapmap]
rs17526884	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2383675	0.87[EUR][1000 genomes]
rs2383677	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34072166	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs3783315	0.96[CEU][hapmap];0.81[CHB][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap]
rs3783316	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs5016735	0.86[EUR][1000 genomes]
rs55979964	0.83[EUR][1000 genomes]
rs56975955	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58074336	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs59092668	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59678582	1.00[ASN][1000 genomes]
rs61981201	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61981204	0.81[ASN][1000 genomes]
rs61988010	0.86[EUR][1000 genomes]
rs6571686	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7148400	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs7150069	0.81[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes]
rs7153289	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7155348	0.84[EUR][1000 genomes]
rs8005470	0.96[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap]
rs8005659	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs8007644	0.97[ASN][1000 genomes]
rs8009900	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8010504	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8010579	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs8013484	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8016548	0.93[ASN][1000 genomes]
rs8017454	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8019856	0.88[CHB][hapmap];0.81[JPT][hapmap]

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	nsv1040980	chr14:34345018-35255592	Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv1048408	chr14:34958352-35255592	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	esv3392700	chr14:34989406-35365530	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	nsv1041857	chr14:35084889-35417180	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1040350	chr14:35196524-35245409	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv1051540	chr14:35200858-35278635	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv517328	chr14:35229680-35234894	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv523492	chr14:35229680-35242828	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17526787	SCFD1	cis	cerebellum	SCAN
rs17526787	NUBPL	cis	parietal	SCAN
rs17526787	SNX6	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:35218200-35232400	Weak transcription	Psoas Muscle	Psoas
2	chr14:35219400-35262000	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr14:35219400-35267000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr14:35219600-35254600	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr14:35219800-35231600	Weak transcription	Right Ventricle	heart
6	chr14:35220200-35231000	Weak transcription	Hela-S3	cervix
7	chr14:35220400-35232200	Weak transcription	HSMMtube	muscle
8	chr14:35221000-35234400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr14:35221000-35234600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr14:35221000-35253200	Strong transcription	Primary B cells from peripheral blood	blood
11	chr14:35221000-35255800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr14:35221200-35231000	Weak transcription	Colon Smooth Muscle	Colon
13	chr14:35221200-35233000	Weak transcription	Brain Anterior Caudate	brain
14	chr14:35221200-35262000	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr14:35221400-35234400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr14:35221400-35234600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr14:35221400-35234600	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr14:35221400-35280800	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr14:35221600-35234400	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr14:35221600-35235400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr14:35221600-35237400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr14:35221600-35237800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr14:35221600-35255400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr14:35221600-35258800	Strong transcription	Dnd41	blood
25	chr14:35221600-35274600	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr14:35222600-35236200	Strong transcription	Primary T cells from cord blood	blood
27	chr14:35222600-35237200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr14:35222800-35232200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr14:35223200-35233600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr14:35223800-35234400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr14:35224000-35240400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr14:35224400-35234400	Strong transcription	Duodenum Mucosa	Duodenum
33	chr14:35224600-35233200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr14:35224600-35233800	Weak transcription	Brain Angular Gyrus	brain
35	chr14:35224600-35234400	Strong transcription	Fetal Intestine Large	intestine
36	chr14:35224600-35234600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr14:35224600-35234800	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr14:35224800-35234600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr14:35225000-35234200	Strong transcription	Fetal Stomach	stomach
40	chr14:35225000-35234400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr14:35225400-35231400	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr14:35225600-35234600	Strong transcription	HUVEC	blood vessel
43	chr14:35225600-35237200	Strong transcription	Fetal Thymus	thymus
44	chr14:35225800-35231800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr14:35225800-35234400	Strong transcription	Fetal Muscle Trunk	muscle
46	chr14:35225800-35234600	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr14:35226000-35234400	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr14:35226000-35273400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr14:35226000-35274000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr14:35226200-35234000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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