Variant report

Variant	rs10008428
Chromosome Location	chr4:107081028-107081029
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10000428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10003024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10004611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10008773	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10016884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10017969	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10018910	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10027207	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10030019	0.96[CEU][hapmap]
rs10049933	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11097912	0.96[CEU][hapmap]
rs11732251	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11732791	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11931386	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11932523	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12509640	0.95[CEU][hapmap]
rs12510966	0.95[CEU][hapmap]
rs12513345	0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs12642691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12650692	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13101612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13113845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13114479	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13121614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13138528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17272618	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2691804	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28394440	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28467469	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28784652	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28805707	0.96[ASN][1000 genomes]
rs28845843	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2949625	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3109953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3109955	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3109958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3109960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3113249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3113250	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3113252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3133168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3133169	0.83[EUR][1000 genomes]
rs4306956	0.88[EUR][1000 genomes]
rs4307042	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4314353	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4355394	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4364267	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4374692	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4382109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4470632	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4508971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4569824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4577583	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4600995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60538413	0.88[EUR][1000 genomes]
rs6533237	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6533242	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6819081	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6835216	0.80[CEU][hapmap]
rs6836198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6842919	0.87[EUR][1000 genomes]
rs6843331	0.88[EUR][1000 genomes]
rs6844105	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6846579	0.95[CEU][hapmap]
rs6849573	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6852388	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6853554	0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs7340989	0.85[AFR][1000 genomes]
rs7356287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.84[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7438546	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7657962	0.95[CEU][hapmap]
rs7657975	0.80[CEU][hapmap]
rs7662592	0.96[CEU][hapmap]
rs7663321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7667596	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7668276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7673101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7678847	0.95[CEU][hapmap]
rs7682646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7687657	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7689298	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7692652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7693333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7693448	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9996093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[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	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	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
3	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
4	esv1799357	chr4:107058025-107099737	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv1801434	chr4:107058025-107099737	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv1800933	chr4:107058025-107118662	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv1802243	chr4:107058025-107118662	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv1802962	chr4:107058025-107118662	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv1803376	chr4:107058025-107118662	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	esv1848076	chr4:107058334-107118662	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv1851828	chr4:107059549-107118662	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10008428	MGC16169	Cis_1M	lymphoblastoid	RTeQTL
rs10008428	SCYE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:107035600-107083200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr4:107038000-107112000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr4:107053800-107083400	Weak transcription	HSMM	muscle
4	chr4:107053800-107083800	Weak transcription	Left Ventricle	heart
5	chr4:107053800-107101600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr4:107054000-107081600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr4:107054000-107083200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:107054000-107083400	Weak transcription	Pancreas	Pancrea
9	chr4:107054000-107091000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:107054000-107113600	Weak transcription	Brain Anterior Caudate	brain
11	chr4:107054200-107083400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:107056200-107083400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr4:107065000-107083400	Weak transcription	Brain Germinal Matrix	brain
14	chr4:107066400-107151200	Weak transcription	Colon Smooth Muscle	Colon
15	chr4:107067400-107083600	Weak transcription	Fetal Kidney	kidney
16	chr4:107067800-107082600	Weak transcription	Fetal Brain Male	brain
17	chr4:107068000-107081200	Weak transcription	Psoas Muscle	Psoas
18	chr4:107068600-107083200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr4:107068600-107083600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:107070200-107083200	Weak transcription	Brain Hippocampus Middle	brain
21	chr4:107070200-107083400	Weak transcription	Fetal Muscle Leg	muscle
22	chr4:107070400-107083200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr4:107070600-107084200	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr4:107071400-107083000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:107071800-107176400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr4:107072000-107083000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:107072200-107083400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr4:107073000-107082800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr4:107073000-107086800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr4:107073400-107083000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr4:107074000-107082600	Weak transcription	Fetal Brain Female	brain
32	chr4:107074200-107114400	Weak transcription	NHDF-Ad	bronchial
33	chr4:107074400-107083400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:107074600-107111800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr4:107075000-107082800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:107075200-107091000	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr4:107075400-107083200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr4:107075800-107114000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr4:107075800-107118200	Weak transcription	Brain Substantia Nigra	brain
40	chr4:107075800-107129600	Weak transcription	Spleen	Spleen
41	chr4:107076000-107081600	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr4:107076000-107083800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr4:107076400-107083600	Weak transcription	Primary B cells from peripheral blood	blood
44	chr4:107076400-107114200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr4:107076800-107083600	Weak transcription	Thymus	Thymus
46	chr4:107077000-107089600	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr4:107077600-107082200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr4:107077600-107083400	Weak transcription	Esophagus	oesophagus
49	chr4:107077800-107083000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr4:107077800-107083200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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