Variant report

Variant	rs7521700
Chromosome Location	chr1:169802760-169802761
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10737549	0.81[ASW][hapmap]
rs10737550	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10737551	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs10800483	0.93[ASW][hapmap];0.81[MEX][hapmap]
rs10800484	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10800485	0.91[CHD][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.86[ASN][1000 genomes]
rs10919257	0.87[EUR][1000 genomes]
rs12047487	0.92[CEU][hapmap]
rs12133843	0.81[MEX][hapmap]
rs2143122	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294496	0.96[CEU][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2901179	0.90[EUR][1000 genomes]
rs3766137	0.80[YRI][hapmap]
rs3766144	0.93[ASW][hapmap];0.96[CEU][hapmap];0.86[TSI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3766148	0.81[ASW][hapmap]
rs3766155	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4508080	0.81[MEX][hapmap]
rs4656197	0.87[ASW][hapmap];1.00[CEU][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4656199	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4656200	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4656724	0.87[ASW][hapmap];1.00[CEU][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs508063	0.85[CEU][hapmap]
rs603246	0.82[CEU][hapmap]
rs6427220	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6427224	0.96[CEU][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6427225	0.81[ASW][hapmap];0.81[MEX][hapmap]
rs6427226	0.90[EUR][1000 genomes]
rs6427227	1.00[CEU][hapmap];0.80[YRI][hapmap];0.90[EUR][1000 genomes]
rs6664099	1.00[CEU][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6668114	0.87[ASW][hapmap];0.92[CEU][hapmap];0.85[TSI][hapmap];0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6670818	0.81[MEX][hapmap]
rs6680938	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6683056	0.81[ASW][hapmap]
rs6684481	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6687377	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7525259	0.81[ASW][hapmap];0.81[MEX][hapmap]
rs7530237	0.81[ASW][hapmap];0.80[YRI][hapmap]
rs9287097	0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv872542	chr1:169802760-169844093	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7521700	C1orf156	cis	cerebellum	SCAN
rs7521700	C1orf156	cis	parietal	SCAN
rs7521700	TADA1	cis	cerebellum	SCAN
rs7521700	SCYL3	cis	cerebellum	SCAN
rs7521700	C1orf112	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169764800-169818200	Weak transcription	Esophagus	oesophagus
2	chr1:169764800-169818200	Weak transcription	Lung	lung
3	chr1:169764800-169823600	Weak transcription	Gastric	stomach
4	chr1:169765000-169808000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:169765000-169821800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:169765200-169807800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:169765200-169808000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:169765200-169809000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr1:169765200-169814800	Weak transcription	Brain Anterior Caudate	brain
10	chr1:169765200-169815200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:169765200-169818800	Weak transcription	Brain Angular Gyrus	brain
12	chr1:169765200-169820600	Weak transcription	Psoas Muscle	Psoas
13	chr1:169765200-169823400	Weak transcription	Right Ventricle	heart
14	chr1:169765400-169808000	Weak transcription	Fetal Heart	heart
15	chr1:169765400-169822600	Weak transcription	Colonic Mucosa	Colon
16	chr1:169765600-169808000	Weak transcription	Small Intestine	intestine
17	chr1:169765600-169818200	Weak transcription	NHLF	lung
18	chr1:169765800-169808000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:169765800-169815200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:169765800-169818400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:169773400-169808000	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:169776400-169808000	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr1:169777400-169815400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:169784000-169814000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:169784000-169814800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr1:169786200-169862400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr1:169786600-169841400	Strong transcription	Dnd41	blood
28	chr1:169788600-169823600	Weak transcription	Pancreas	Pancrea
29	chr1:169789200-169818600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:169790400-169808000	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:169790800-169803200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:169790800-169804600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr1:169790800-169808000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr1:169790800-169808800	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:169791000-169804600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:169791200-169802800	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr1:169791200-169803000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:169791200-169804200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:169791200-169808800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr1:169791200-169810800	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr1:169791200-169841200	Strong transcription	Fetal Thymus	thymus
42	chr1:169793800-169808000	Weak transcription	Brain Hippocampus Middle	brain
43	chr1:169793800-169808000	Weak transcription	Fetal Brain Male	brain
44	chr1:169793800-169814400	Weak transcription	Brain Substantia Nigra	brain
45	chr1:169793800-169822600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr1:169794000-169814800	Weak transcription	Aorta	Aorta
47	chr1:169794200-169808000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr1:169794200-169818400	Weak transcription	NHEK	skin
49	chr1:169794800-169822000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr1:169795800-169802800	Strong transcription	Placenta	Placenta

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