Variant report

Variant	rs10016884
Chromosome Location	chr4:107120677-107120678
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 150 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs10000428	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10003024	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10004611	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10008428	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10008773	0.86[ASN][1000 genomes]
rs10017969	0.99[ASN][1000 genomes]
rs10018910	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.99[ASN][1000 genomes]
rs10027207	0.99[ASN][1000 genomes]
rs10049933	1.00[ASN][1000 genomes]
rs10433894	0.95[CEU][hapmap]
rs10516532	0.95[CEU][hapmap]
rs10516533	1.00[CEU][hapmap]
rs10516534	0.95[CEU][hapmap]
rs11097917	0.94[CEU][hapmap]
rs11097919	0.86[ASW][hapmap];0.95[CEU][hapmap]
rs11097924	0.95[CEU][hapmap]
rs11097925	0.95[CEU][hapmap]
rs11097927	0.95[CEU][hapmap]
rs11732251	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11732791	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11931386	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11932523	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12504704	0.95[CEU][hapmap]
rs12504721	0.95[CEU][hapmap]
rs12506062	0.86[ASW][hapmap];0.95[CEU][hapmap]
rs12507429	0.86[ASW][hapmap];0.95[CEU][hapmap]
rs12508432	0.95[CEU][hapmap]
rs12509865	0.95[CEU][hapmap]
rs12511305	0.86[ASW][hapmap];0.95[CEU][hapmap]
rs12512877	0.95[CEU][hapmap]
rs12512903	0.95[CEU][hapmap]
rs12512966	0.86[ASW][hapmap];0.95[CEU][hapmap]
rs12513317	0.95[CEU][hapmap]
rs12513345	0.85[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs12639869	0.95[CEU][hapmap]
rs12641015	0.86[ASW][hapmap];0.95[CEU][hapmap]
rs12641037	0.95[CEU][hapmap]
rs12642059	0.94[CEU][hapmap]
rs12642227	0.82[AFR][1000 genomes]
rs12642454	0.95[CEU][hapmap]
rs12642691	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[ASN][1000 genomes]
rs12644259	0.95[CEU][hapmap]
rs12645271	0.95[CEU][hapmap]
rs12648091	0.82[CEU][hapmap]
rs12650692	0.94[ASN][1000 genomes]
rs12651360	0.94[CEU][hapmap]
rs13101612	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13113845	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13114479	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs13121614	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13138528	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17036613	0.93[ASW][hapmap];0.86[LWK][hapmap];0.83[MKK][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes]
rs17272618	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]
rs17273093	0.95[CEU][hapmap]
rs17274017	0.95[CEU][hapmap]
rs17274248	0.95[CEU][hapmap]
rs17333287	0.95[CEU][hapmap]
rs17333732	0.95[CEU][hapmap]
rs17333879	0.95[CEU][hapmap]
rs17333899	0.95[CEU][hapmap]
rs2290607	0.95[CEU][hapmap]
rs2691804	0.96[ASN][1000 genomes]
rs28394440	0.90[ASN][1000 genomes]
rs28467469	0.99[ASN][1000 genomes]
rs28784652	0.96[ASN][1000 genomes]
rs28805707	0.98[ASN][1000 genomes]
rs28845843	0.99[ASN][1000 genomes]
rs2949625	0.95[ASN][1000 genomes]
rs3109953	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3109955	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs3109958	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3109960	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3113249	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3113250	0.97[ASN][1000 genomes]
rs3113252	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3133168	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3737497	0.95[CEU][hapmap]
rs3737498	0.95[CEU][hapmap]
rs3762945	0.95[CEU][hapmap]
rs3762947	0.95[CEU][hapmap]
rs3775090	0.95[CEU][hapmap]
rs3805409	0.95[CEU][hapmap]
rs3805410	0.95[CEU][hapmap]
rs3805411	0.95[CEU][hapmap]
rs4307042	0.99[ASN][1000 genomes]
rs4314353	0.99[ASN][1000 genomes]
rs4355394	0.86[ASN][1000 genomes]
rs4364267	0.85[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs4374692	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4382109	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4429790	0.95[CEU][hapmap]
rs4458525	0.95[CEU][hapmap]
rs4470632	0.90[ASN][1000 genomes]
rs4508971	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4569824	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4577583	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4600995	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6533237	0.86[ASN][1000 genomes]
rs6533240	0.94[CEU][hapmap]
rs6533242	0.92[ASN][1000 genomes]
rs6533243	0.95[CEU][hapmap]
rs6533245	0.95[CEU][hapmap];0.81[TSI][hapmap]
rs6533246	0.95[CEU][hapmap]
rs6814166	0.95[CEU][hapmap]
rs6815014	0.94[CEU][hapmap]
rs6816698	0.95[CEU][hapmap]
rs6818197	0.86[ASW][hapmap];0.95[CEU][hapmap]
rs6819081	0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.97[ASN][1000 genomes]
rs6819224	0.95[CEU][hapmap]
rs6831032	0.95[CEU][hapmap]
rs6836198	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6838283	0.95[CEU][hapmap]
rs6843870	0.95[CEU][hapmap]
rs6844105	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6849341	0.95[CEU][hapmap]
rs6849573	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.99[ASN][1000 genomes]
rs6852388	0.99[ASN][1000 genomes]
rs6853554	0.85[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.86[ASN][1000 genomes]
rs6856408	0.95[CEU][hapmap]
rs6858391	0.95[CEU][hapmap]
rs72876575	0.85[AFR][1000 genomes]
rs7356287	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7438546	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7661565	0.95[CEU][hapmap]
rs7662219	0.95[CEU][hapmap]
rs7662291	0.95[CEU][hapmap]
rs7662395	0.95[CEU][hapmap]
rs7663321	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7665946	0.95[CEU][hapmap]
rs7667596	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7668276	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7668477	0.95[CEU][hapmap]
rs7673101	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7673949	0.95[CEU][hapmap]
rs7678229	0.95[CEU][hapmap]
rs7681257	0.95[CEU][hapmap]
rs7682646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7687657	0.84[ASN][1000 genomes]
rs7688008	0.95[CEU][hapmap]
rs7688411	0.95[CEU][hapmap]
rs7689298	0.93[ASN][1000 genomes]
rs7692652	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7693333	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7693448	0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs7699768	0.95[CEU][hapmap]
rs9996093	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[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	nsv879701	chr4:107024776-107163128	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv879702	chr4:107065718-107175191	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv879703	chr4:107082926-107163128	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv879704	chr4:107095901-107212966	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10016884	MGC16169	cis	multi-tissue	Pritchard
rs10016884	MGC16169	Cis_1M	lymphoblastoid	RTeQTL
rs10016884	TBCK	cis	cerebellum	SCAN
rs10016884	TBCK	cis	parietal	SCAN
rs10016884	TBCK	cis	lymphoblastoid	seeQTL
rs10016884	SCYE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:107066400-107151200	Weak transcription	Colon Smooth Muscle	Colon
2	chr4:107071800-107176400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:107075800-107129600	Weak transcription	Spleen	Spleen
4	chr4:107083200-107173400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr4:107083800-107134000	Weak transcription	Right Ventricle	heart
6	chr4:107083800-107164800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:107084000-107129800	Weak transcription	Lung	lung
8	chr4:107084200-107129600	Weak transcription	Aorta	Aorta
9	chr4:107084400-107141400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr4:107085000-107129600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr4:107085000-107150000	Weak transcription	Dnd41	blood
12	chr4:107085400-107169600	Weak transcription	Fetal Kidney	kidney
13	chr4:107087200-107129800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr4:107088400-107166400	Weak transcription	K562	blood
15	chr4:107091200-107129200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr4:107091400-107129800	Weak transcription	Pancreas	Pancrea
17	chr4:107104600-107140800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:107105000-107169600	Weak transcription	Fetal Brain Female	brain
19	chr4:107106800-107176400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr4:107107000-107149600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr4:107107200-107130000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr4:107108800-107129600	Weak transcription	Fetal Muscle Leg	muscle
23	chr4:107111800-107160200	Weak transcription	NHEK	skin
24	chr4:107112400-107129400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr4:107112400-107170400	Weak transcription	Thymus	Thymus
26	chr4:107112600-107129600	Weak transcription	Gastric	stomach
27	chr4:107113000-107150800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr4:107113000-107154800	Weak transcription	Brain Angular Gyrus	brain
29	chr4:107113200-107130800	Weak transcription	HSMM	muscle
30	chr4:107113400-107150200	Weak transcription	Osteobl	bone
31	chr4:107113600-107133400	Weak transcription	Fetal Lung	lung
32	chr4:107114400-107149200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr4:107114600-107127600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr4:107114600-107149600	Weak transcription	HSMMtube	muscle
35	chr4:107114600-107236000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr4:107114800-107127400	Weak transcription	Adipose Nuclei	Adipose
37	chr4:107114800-107129200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr4:107114800-107129400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:107114800-107129400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr4:107114800-107129400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr4:107114800-107129400	Weak transcription	Fetal Thymus	thymus
42	chr4:107114800-107129600	Weak transcription	Primary B cells from cord blood	blood
43	chr4:107114800-107129600	Weak transcription	Left Ventricle	heart
44	chr4:107114800-107129600	Weak transcription	Ovary	ovary
45	chr4:107114800-107129800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr4:107114800-107129800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr4:107114800-107131400	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr4:107114800-107133400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr4:107114800-107133400	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr4:107114800-107133600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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