Variant report

Variant	rs2271520
Chromosome Location	chr17:17035036-17035037
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10852847	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11078374	1.00[CHB][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11656868	1.00[CHB][hapmap]
rs11871902	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2090018	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2349646	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28461224	1.00[ASN][1000 genomes]
rs4247118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4247120	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4275914	1.00[ASN][1000 genomes]
rs4514740	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4985696	1.00[ASN][1000 genomes]
rs4985701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985702	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985717	1.00[ASN][1000 genomes]
rs4985718	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4985740	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.91[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4985746	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985778	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6502563	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7206981	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207485	1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7208929	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7208973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7217091	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7220827	1.00[CHB][hapmap]
rs7221842	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7222311	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8064550	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[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]
rs8072184	1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8073842	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8079563	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9893911	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9898995	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9908767	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9914671	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907728	chr17:17013189-17095487	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv984510	chr17:17015688-17048858	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv524958	chr17:17029718-17060805	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2271520	RNF112	cis	cerebellum	SCAN
rs2271520	TOM1L2	cis	cerebellum	SCAN
rs2271520	FLCN	cis	cerebellum	SCAN
rs2271520	ULK2	cis	cerebellum	SCAN
rs2271520	TRPV2	cis	cerebellum	SCAN
rs2271520	FLCN	cis	parietal	SCAN
rs2271520	UBB	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17012000-17035200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr17:17015400-17035200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr17:17024200-17043200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr17:17024400-17039800	Weak transcription	Small Intestine	intestine
5	chr17:17024600-17036000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr17:17024600-17045600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr17:17027400-17042400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr17:17027400-17043000	Strong transcription	NHEK	skin
9	chr17:17027400-17043400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr17:17028000-17038200	Genic enhancers	Fetal Muscle Trunk	muscle
11	chr17:17028200-17036600	Genic enhancers	Fetal Muscle Leg	muscle
12	chr17:17029800-17035400	Genic enhancers	Right Ventricle	heart
13	chr17:17029800-17043400	Strong transcription	NHLF	lung
14	chr17:17029800-17044200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr17:17029800-17088400	Strong transcription	Dnd41	blood
16	chr17:17030000-17041800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr17:17030000-17042800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr17:17030000-17042800	Strong transcription	A549	lung
19	chr17:17030000-17043200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr17:17030000-17043200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr17:17030000-17043600	Strong transcription	Esophagus	oesophagus
22	chr17:17030000-17048200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr17:17030000-17052200	Strong transcription	Primary B cells from peripheral blood	blood
24	chr17:17030000-17088000	Strong transcription	Duodenum Mucosa	Duodenum
25	chr17:17030200-17035200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr17:17030200-17035600	Strong transcription	Aorta	Aorta
27	chr17:17030200-17037000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr17:17030200-17037400	Strong transcription	Colon Smooth Muscle	Colon
29	chr17:17030200-17037400	Strong transcription	Rectal Smooth Muscle	rectum
30	chr17:17030200-17037800	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr17:17030200-17042800	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr17:17030200-17043800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr17:17030200-17051600	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr17:17030200-17055000	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr17:17030400-17035200	Weak transcription	Fetal Brain Male	brain
36	chr17:17030400-17038800	Genic enhancers	Brain Hippocampus Middle	brain
37	chr17:17030400-17043800	Strong transcription	Adipose Nuclei	Adipose
38	chr17:17030400-17044800	Strong transcription	Primary B cells from cord blood	blood
39	chr17:17030400-17047600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr17:17030400-17047800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr17:17030400-17055800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr17:17030400-17059800	Strong transcription	Fetal Intestine Small	intestine
43	chr17:17030400-17079200	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr17:17030400-17089200	Strong transcription	Fetal Intestine Large	intestine
45	chr17:17030600-17040600	Genic enhancers	Brain Anterior Caudate	brain
46	chr17:17030600-17042800	Strong transcription	Osteobl	bone
47	chr17:17030600-17045000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr17:17030600-17051000	Strong transcription	Colonic Mucosa	Colon
49	chr17:17030800-17038800	Genic enhancers	Brain Angular Gyrus	brain
50	chr17:17030800-17042800	Strong transcription	Thymus	Thymus

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