Variant report

Variant	rs10017969
Chromosome Location	chr4:107054085-107054086
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10000428	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10003024	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10004611	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10008428	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10008773	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10016884	0.99[ASN][1000 genomes]
rs10018910	0.99[ASN][1000 genomes]
rs10025668	0.82[AFR][1000 genomes]
rs10027207	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10049933	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11732251	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11732791	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11931386	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11932523	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12513345	0.87[ASN][1000 genomes]
rs12642691	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12650692	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13101612	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13113845	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13114479	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13121614	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13138528	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17272618	0.99[ASN][1000 genomes]
rs2691804	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28394440	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28418378	0.80[AFR][1000 genomes]
rs28467469	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28784652	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28805707	0.99[ASN][1000 genomes]
rs28845843	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2949625	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3109953	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3109955	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3109958	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3109960	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3113249	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3113250	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3113252	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3133168	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3133169	0.83[EUR][1000 genomes]
rs4306956	0.87[EUR][1000 genomes]
rs4307042	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4314353	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4355394	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4364267	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4374692	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4382109	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4470632	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4508971	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4569824	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4577583	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4600995	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60538413	0.87[EUR][1000 genomes]
rs6533237	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6533242	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6819081	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6836198	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6842919	0.87[EUR][1000 genomes]
rs6843331	0.88[EUR][1000 genomes]
rs6844105	0.99[ASN][1000 genomes]
rs6849573	0.99[ASN][1000 genomes]
rs6852388	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6853554	0.87[ASN][1000 genomes]
rs7356287	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7438546	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7667596	0.96[ASN][1000 genomes]
rs7668276	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7673101	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7682646	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7687657	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7689298	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7692652	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7693333	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7693448	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9991203	0.82[AFR][1000 genomes]
rs9996093	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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
5	nsv511247	chr4:107022702-107065220	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	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
7	nsv4450	chr4:107037823-107082669	Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv508301	chr4:107049086-107092730	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	esv1851766	chr4:107052107-107062671	ZNF genes & repeats Strong transcription Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv437409	chr4:107052107-107064347	Weak transcription ZNF genes & repeats Enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv437410	chr4:107052107-107064347	Weak transcription Strong transcription ZNF genes & repeats Enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv437411	chr4:107052107-107074097	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10017969	SCYE1	Cis_1M	lymphoblastoid	RTeQTL
rs10017969	MGC16169	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:107032000-107058200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:107035200-107057200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:107035600-107083200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:107037600-107056200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr4:107037600-107060600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr4:107037600-107061600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr4:107037600-107066400	Weak transcription	Fetal Kidney	kidney
8	chr4:107037800-107077400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:107038000-107055400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:107038000-107056800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr4:107038000-107112000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr4:107051800-107054800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr4:107052800-107054600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:107053000-107054200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
15	chr4:107053000-107054200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
16	chr4:107053000-107054400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
17	chr4:107053000-107055200	ZNF genes & repeats	Fetal Intestine Small	intestine
18	chr4:107053200-107055200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr4:107053400-107054200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
20	chr4:107053400-107054200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:107053400-107054200	ZNF genes & repeats	Adipose Nuclei	Adipose
22	chr4:107053400-107054600	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr4:107053400-107054600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
24	chr4:107053400-107055200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr4:107053400-107056200	Strong transcription	Ovary	ovary
26	chr4:107053600-107055200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr4:107053600-107067600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr4:107053800-107058200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:107053800-107061400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:107053800-107064200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr4:107053800-107070000	Weak transcription	Brain Hippocampus Middle	brain
32	chr4:107053800-107080000	Weak transcription	Right Ventricle	heart
33	chr4:107053800-107083400	Weak transcription	HSMM	muscle
34	chr4:107053800-107083800	Weak transcription	Left Ventricle	heart
35	chr4:107053800-107101600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr4:107054000-107054200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr4:107054000-107054200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:107054000-107054600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr4:107054000-107054600	Weak transcription	Thymus	Thymus
40	chr4:107054000-107055200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr4:107054000-107055400	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr4:107054000-107055600	Weak transcription	Primary B cells from cord blood	blood
43	chr4:107054000-107055600	Weak transcription	Primary T cells from cord blood	blood
44	chr4:107054000-107055600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr4:107054000-107055600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr4:107054000-107057600	Weak transcription	Brain Substantia Nigra	brain
47	chr4:107054000-107057800	Weak transcription	Fetal Thymus	thymus
48	chr4:107054000-107057800	Weak transcription	Dnd41	blood
49	chr4:107054000-107063400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr4:107054000-107066400	Weak transcription	Liver	Liver

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