Variant report

Variant	rs1038202
Chromosome Location	chr3:43585255-43585256
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:43585068..43586639-chr3:43731094..43733341,2	K562	blood:
2	chr3:43585085..43587438-chr3:43589479..43591274,2	K562	blood:

Variant related genes	Relation type
ENSG00000160746	Chromatin interaction
ENSG00000011198	Chromatin interaction

Extended variants
information (count: 152 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:147)

rs_ID	r²[population]
rs1013758	0.81[EUR][1000 genomes]
rs1021049	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[ASN][1000 genomes]
rs1026887	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10440111	0.82[ASN][1000 genomes]
rs10461013	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs11130004	0.85[CEU][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs11130005	0.84[EUR][1000 genomes]
rs11130006	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11706123	0.87[ASN][1000 genomes]
rs11706130	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11708097	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11709165	0.89[ASN][1000 genomes]
rs11710079	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11710107	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11710955	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11711758	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11712894	0.89[ASN][1000 genomes]
rs11713382	0.91[ASN][1000 genomes]
rs11714015	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.96[ASN][1000 genomes]
rs11715896	1.00[CEU][hapmap];0.92[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs11716569	0.93[ASN][1000 genomes]
rs11717380	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11717449	0.91[ASN][1000 genomes]
rs11718482	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12152260	0.84[ASN][1000 genomes]
rs12374079	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12486736	0.87[EUR][1000 genomes]
rs12638282	0.85[CEU][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs13061553	0.89[ASN][1000 genomes]
rs13072613	0.96[ASN][1000 genomes]
rs13075520	0.96[ASN][1000 genomes]
rs13079636	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13084604	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs13086999	0.93[ASN][1000 genomes]
rs13092838	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.96[ASN][1000 genomes]
rs13097209	0.87[ASN][1000 genomes]
rs13098202	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs1351631	0.85[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs1384434	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1384435	0.85[CEU][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs1471643	0.91[ASN][1000 genomes]
rs1471644	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs1482648	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs1482649	0.93[ASN][1000 genomes]
rs1482650	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1482651	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[ASN][1000 genomes]
rs1482652	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs1482653	0.84[ASN][1000 genomes]
rs1506616	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1564434	0.85[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs17030517	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17407745	0.91[ASN][1000 genomes]
rs17407870	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs17407912	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs17408925	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17643558	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1842806	0.81[EUR][1000 genomes]
rs1975997	0.85[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs2010778	0.93[ASN][1000 genomes]
rs2054552	0.89[ASN][1000 genomes]
rs2054553	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2054554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2086653	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[ASN][1000 genomes]
rs2101064	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs2127725	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2170219	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[ASN][1000 genomes]
rs2199892	0.93[ASN][1000 genomes]
rs2219902	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs2372433	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs2372436	0.93[ASN][1000 genomes]
rs2372487	0.96[ASN][1000 genomes]
rs2888312	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs34279519	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34548104	0.91[ASN][1000 genomes]
rs34898315	0.91[ASN][1000 genomes]
rs34919938	0.86[ASN][1000 genomes]
rs35015014	0.91[ASN][1000 genomes]
rs35133889	0.93[ASN][1000 genomes]
rs35323779	0.82[ASN][1000 genomes]
rs35418463	0.93[ASN][1000 genomes]
rs3755602	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs3772160	0.84[EUR][1000 genomes]
rs3772165	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3772167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs3774790	0.85[CHD][hapmap]
rs3821381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3902207	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4128530	0.81[CEU][hapmap]
rs4234430	1.00[JPT][hapmap]
rs4264704	0.83[EUR][1000 genomes]
rs4407383	0.82[CEU][hapmap]
rs4432612	0.94[CHD][hapmap]
rs4505672	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs4547674	0.81[CEU][hapmap]
rs4564953	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4682690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4682691	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[ASN][1000 genomes]
rs4682892	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.96[ASN][1000 genomes]
rs4682894	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4682897	0.84[ASN][1000 genomes]
rs4682898	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4682900	0.85[CHD][hapmap]
rs61102363	0.82[EUR][1000 genomes]
rs6441775	0.83[ASN][1000 genomes]
rs6441776	0.93[ASN][1000 genomes]
rs6441779	0.94[ASN][1000 genomes]
rs6441780	0.96[ASN][1000 genomes]
rs6441781	0.93[ASN][1000 genomes]
rs6441785	0.85[ASN][1000 genomes]
rs6441786	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6441787	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs66842319	0.93[ASN][1000 genomes]
rs67032102	0.91[ASN][1000 genomes]
rs6763321	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6767983	0.91[ASN][1000 genomes]
rs6768557	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs6775337	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6779864	0.84[ASN][1000 genomes]
rs6781290	0.89[ASN][1000 genomes]
rs6782442	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[ASN][1000 genomes]
rs6786013	0.81[AMR][1000 genomes]
rs6797855	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6806339	0.85[ASN][1000 genomes]
rs6809134	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.96[ASN][1000 genomes]
rs737516	0.85[CEU][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs7428158	0.81[CHB][hapmap];0.90[CHD][hapmap];0.85[ASN][1000 genomes]
rs7616708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7621271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7630010	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs7648082	0.84[ASN][1000 genomes]
rs7653738	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs9311340	0.92[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs9311341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9682975	0.91[ASN][1000 genomes]
rs9809643	0.85[EUR][1000 genomes]
rs9814737	0.86[EUR][1000 genomes]
rs9815196	0.85[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs9824990	0.81[CEU][hapmap]
rs9829067	0.87[EUR][1000 genomes]
rs9829081	0.96[ASN][1000 genomes]
rs9830697	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs9835793	0.83[EUR][1000 genomes]
rs9851894	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9863479	0.93[ASN][1000 genomes]
rs9873316	0.86[EUR][1000 genomes]
rs9878330	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9881028	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428738	chr3:43491435-43651168	Strong transcription Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv822067	chr3:43584576-43592360	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv822068	chr3:43584795-43592360	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv822069	chr3:43585009-43592360	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv822070	chr3:43585009-43596684	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1038202	SNRK	cis	cerebellum	SCAN
rs1038202	RPL14	cis	parietal	SCAN
rs1038202	C3orf39	cis	cerebellum	SCAN
rs1038202	ANO10	cis	Whole Blood	GTEx
rs1038202	MRPS18A	trans	cerebellum	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43540200-43602200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:43542800-43588800	Weak transcription	Left Ventricle	heart
3	chr3:43544000-43617600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:43547600-43595800	Weak transcription	Fetal Stomach	stomach
5	chr3:43553000-43601600	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:43553600-43595800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:43554800-43589400	Weak transcription	HSMMtube	muscle
8	chr3:43556200-43624800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:43558600-43625600	Weak transcription	Lung	lung
10	chr3:43560800-43618000	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:43561200-43601200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:43561400-43600400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:43561600-43588800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:43561600-43589000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr3:43561600-43590600	Weak transcription	Ovary	ovary
16	chr3:43561600-43601000	Weak transcription	Pancreas	Pancrea
17	chr3:43561800-43590600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:43561800-43602000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:43562000-43589200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr3:43569600-43587800	Weak transcription	Primary T cells from cord blood	blood
21	chr3:43571000-43588000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr3:43571000-43594600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:43571000-43613600	Weak transcription	Gastric	stomach
24	chr3:43573800-43596400	Weak transcription	HMEC	breast
25	chr3:43573800-43601400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:43573800-43617800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:43574800-43662400	Weak transcription	Right Ventricle	heart
28	chr3:43576200-43586800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:43576200-43601000	Weak transcription	Esophagus	oesophagus
30	chr3:43576200-43623800	Weak transcription	Psoas Muscle	Psoas
31	chr3:43576400-43589000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:43576400-43613600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:43576400-43621200	Weak transcription	NHEK	skin
34	chr3:43577000-43590800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:43577200-43595400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:43577400-43590600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:43577600-43625400	Weak transcription	HUVEC	blood vessel
38	chr3:43577800-43595000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:43578200-43599800	Weak transcription	Fetal Brain Female	brain
40	chr3:43578400-43593400	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr3:43579000-43589200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr3:43579000-43590400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:43579000-43594600	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr3:43579200-43590800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:43579200-43600200	Weak transcription	Liver	Liver
46	chr3:43580600-43647600	Weak transcription	Brain Angular Gyrus	brain
47	chr3:43580800-43613800	Weak transcription	Aorta	Aorta
48	chr3:43581000-43586400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:43581000-43589000	Weak transcription	HSMM	muscle
50	chr3:43581200-43589000	Weak transcription	Monocytes-CD14+_RO01746	blood

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