Variant report

Variant	rs17272618
Chromosome Location	chr4:107022503-107022504
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10000428	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs10002288	0.80[EUR][1000 genomes]
rs10003024	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs10004611	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs10008428	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs10008773	0.88[ASN][1000 genomes]
rs10016884	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.99[ASN][1000 genomes]
rs10017969	0.99[ASN][1000 genomes]
rs10018910	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10027207	0.98[ASN][1000 genomes]
rs10049933	0.99[ASN][1000 genomes]
rs10084928	0.93[ASW][hapmap];0.95[CEU][hapmap];0.94[LWK][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs10516533	0.81[CEU][hapmap]
rs11725254	0.93[EUR][1000 genomes]
rs11732251	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs11732791	0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs11931386	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs11932523	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs12508552	0.82[EUR][1000 genomes]
rs12513345	0.95[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12639678	0.92[EUR][1000 genomes]
rs12642691	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.96[ASN][1000 genomes]
rs12643397	0.87[AFR][1000 genomes]
rs12650692	0.92[ASN][1000 genomes]
rs13101612	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs13113845	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs13114479	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs13121614	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs13138528	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs17333287	0.81[CEU][hapmap]
rs28394440	0.92[ASN][1000 genomes]
rs28467469	1.00[ASN][1000 genomes]
rs28507027	0.82[EUR][1000 genomes]
rs28765420	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs28784652	0.97[ASN][1000 genomes]
rs28787305	0.82[EUR][1000 genomes]
rs28805707	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28845843	1.00[ASN][1000 genomes]
rs28866820	0.82[EUR][1000 genomes]
rs28868894	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs28875879	0.80[EUR][1000 genomes]
rs3109953	0.94[ASN][1000 genomes]
rs3109955	0.94[ASN][1000 genomes]
rs3109958	0.96[ASN][1000 genomes]
rs3109960	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs3113249	0.95[ASN][1000 genomes]
rs3113250	0.83[CEU][hapmap];0.96[ASN][1000 genomes]
rs3113252	0.94[ASN][1000 genomes]
rs3133168	0.94[ASN][1000 genomes]
rs4307042	0.99[ASN][1000 genomes]
rs4314353	1.00[ASN][1000 genomes]
rs4323181	0.82[EUR][1000 genomes]
rs4337798	0.81[EUR][1000 genomes]
rs4339284	0.87[AFR][1000 genomes]
rs4355394	0.87[ASN][1000 genomes]
rs4364267	0.85[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs4374692	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs4382109	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs4470632	0.92[ASN][1000 genomes]
rs4508971	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs4521418	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4569824	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs4577583	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs4600995	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.99[ASN][1000 genomes]
rs6533237	0.88[ASN][1000 genomes]
rs6533242	0.91[ASN][1000 genomes]
rs6810877	0.85[AFR][1000 genomes]
rs6816614	0.87[AFR][1000 genomes]
rs6819081	0.83[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.80[JPT][hapmap];0.96[ASN][1000 genomes]
rs6829795	0.95[CEU][hapmap];0.81[TSI][hapmap]
rs6835216	0.95[CEU][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6836198	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.99[ASN][1000 genomes]
rs6844105	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6844324	0.80[EUR][1000 genomes]
rs6849573	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6852388	1.00[ASN][1000 genomes]
rs6853554	0.86[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7356287	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs7438546	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs7657975	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs7658011	0.80[EUR][1000 genomes]
rs7662806	0.80[EUR][1000 genomes]
rs7663321	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7664188	0.95[CEU][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7667596	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs7668276	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs7669087	0.95[CEU][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs7671145	0.93[ASW][hapmap];0.95[CEU][hapmap];0.93[LWK][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7673101	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs7682646	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs7687657	0.85[ASN][1000 genomes]
rs7689298	0.94[ASN][1000 genomes]
rs7692652	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7693333	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs7693448	0.90[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs7698386	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9996093	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1799793	chr4:107000462-107062671	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv1801716	chr4:107000462-107062671	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv1849248	chr4:107000462-107062671	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv1850577	chr4:107000462-107062671	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17272618	MGC16169	Cis_1M	lymphoblastoid	RTeQTL
rs17272618	SCYE1	Cis_1M	lymphoblastoid	RTeQTL
rs17272618	TBCK	cis	lymphoblastoid	seeQTL
rs17272618	TBCK	cis	parietal	SCAN
rs17272618	MGC16169	cis	multi-tissue	Pritchard

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106997200-107031000	Weak transcription	Psoas Muscle	Psoas
2	chr4:107010200-107025400	Weak transcription	Small Intestine	intestine
3	chr4:107012400-107024400	Weak transcription	Fetal Heart	heart
4	chr4:107012400-107026800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr4:107012600-107025000	Weak transcription	Brain Substantia Nigra	brain
6	chr4:107012600-107025200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:107012600-107026200	Weak transcription	Stomach Mucosa	stomach
8	chr4:107012600-107026600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr4:107012600-107026600	Weak transcription	GM12878-XiMat	blood
10	chr4:107012600-107026600	Weak transcription	HSMM	muscle
11	chr4:107012600-107026800	Weak transcription	Fetal Kidney	kidney
12	chr4:107012600-107029800	Weak transcription	Fetal Brain Male	brain
13	chr4:107012600-107029800	Weak transcription	Dnd41	blood
14	chr4:107012600-107031200	Weak transcription	Brain Angular Gyrus	brain
15	chr4:107012600-107033200	Weak transcription	Osteobl	bone
16	chr4:107012600-107033800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr4:107012600-107034400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:107012600-107038400	Weak transcription	NHDF-Ad	bronchial
19	chr4:107012800-107024600	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr4:107012800-107024600	Weak transcription	Brain Anterior Caudate	brain
21	chr4:107012800-107024800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:107012800-107024800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr4:107012800-107024800	Weak transcription	Brain Hippocampus Middle	brain
24	chr4:107012800-107024800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr4:107012800-107025400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr4:107012800-107025400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr4:107012800-107026200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr4:107012800-107030600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr4:107012800-107031400	Weak transcription	HSMMtube	muscle
30	chr4:107012800-107033400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr4:107013000-107024600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr4:107013000-107031000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr4:107014000-107024600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr4:107014000-107024800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr4:107014000-107029800	Weak transcription	Brain Germinal Matrix	brain
36	chr4:107014000-107031000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:107014000-107031000	Weak transcription	Fetal Thymus	thymus
38	chr4:107014000-107031200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr4:107014000-107034600	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr4:107014200-107024800	Weak transcription	Esophagus	oesophagus
41	chr4:107014200-107024800	Weak transcription	Fetal Intestine Large	intestine
42	chr4:107014200-107024800	Weak transcription	Placenta	Placenta
43	chr4:107014200-107024800	Weak transcription	Thymus	Thymus
44	chr4:107014200-107024800	Weak transcription	Spleen	Spleen
45	chr4:107014200-107025000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr4:107014200-107025000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr4:107014200-107025000	Weak transcription	Aorta	Aorta
48	chr4:107014200-107025000	Weak transcription	Lung	lung
49	chr4:107014200-107025200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr4:107014200-107026000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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