Variant report

Variant	rs4985702
Chromosome Location	chr17:17037222-17037223
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 8 )

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];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2090018	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271520	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]
rs2349646	0.90[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];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[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	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];0.83[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];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4985746	0.96[AMR][1000 genomes];0.85[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];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7206981	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207485	1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7208929	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7208973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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];0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7220827	1.00[CHB][hapmap]
rs7221842	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7222311	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9898995	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9908767	0.89[AMR][1000 genomes];0.92[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4985702	RNF112	cis	cerebellum	SCAN
rs4985702	TOM1L2	cis	cerebellum	SCAN
rs4985702	FLCN	cis	parietal	SCAN
rs4985702	UBB	cis	cerebellum	SCAN
rs4985702	FLCN	cis	cerebellum	SCAN
rs4985702	M-RIP	cis	multi-tissue	Pritchard
rs4985702	ULK2	cis	cerebellum	SCAN
rs4985702	TRPV2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17024200-17043200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr17:17024400-17039800	Weak transcription	Small Intestine	intestine
3	chr17:17024600-17045600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr17:17027400-17042400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr17:17027400-17043000	Strong transcription	NHEK	skin
6	chr17:17027400-17043400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr17:17028000-17038200	Genic enhancers	Fetal Muscle Trunk	muscle
8	chr17:17029800-17043400	Strong transcription	NHLF	lung
9	chr17:17029800-17044200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr17:17029800-17088400	Strong transcription	Dnd41	blood
11	chr17:17030000-17041800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr17:17030000-17042800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr17:17030000-17042800	Strong transcription	A549	lung
14	chr17:17030000-17043200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr17:17030000-17043200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr17:17030000-17043600	Strong transcription	Esophagus	oesophagus
17	chr17:17030000-17048200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr17:17030000-17052200	Strong transcription	Primary B cells from peripheral blood	blood
19	chr17:17030000-17088000	Strong transcription	Duodenum Mucosa	Duodenum
20	chr17:17030200-17037400	Strong transcription	Colon Smooth Muscle	Colon
21	chr17:17030200-17037400	Strong transcription	Rectal Smooth Muscle	rectum
22	chr17:17030200-17037800	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr17:17030200-17042800	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr17:17030200-17043800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr17:17030200-17051600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr17:17030200-17055000	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr17:17030400-17038800	Genic enhancers	Brain Hippocampus Middle	brain
28	chr17:17030400-17043800	Strong transcription	Adipose Nuclei	Adipose
29	chr17:17030400-17044800	Strong transcription	Primary B cells from cord blood	blood
30	chr17:17030400-17047600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr17:17030400-17047800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr17:17030400-17055800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr17:17030400-17059800	Strong transcription	Fetal Intestine Small	intestine
34	chr17:17030400-17079200	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr17:17030400-17089200	Strong transcription	Fetal Intestine Large	intestine
36	chr17:17030600-17040600	Genic enhancers	Brain Anterior Caudate	brain
37	chr17:17030600-17042800	Strong transcription	Osteobl	bone
38	chr17:17030600-17045000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr17:17030600-17051000	Strong transcription	Colonic Mucosa	Colon
40	chr17:17030800-17038800	Genic enhancers	Brain Angular Gyrus	brain
41	chr17:17030800-17042800	Strong transcription	Thymus	Thymus
42	chr17:17030800-17043400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr17:17031000-17040000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr17:17031000-17043600	Strong transcription	HSMM	muscle
45	chr17:17031000-17078800	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr17:17031200-17038000	Strong transcription	Fetal Brain Female	brain
47	chr17:17031200-17057200	Strong transcription	Primary T cells from cord blood	blood
48	chr17:17031200-17067800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr17:17031400-17042400	Strong transcription	Ovary	ovary
50	chr17:17031400-17051800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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