Variant report

Variant	rs951613
Chromosome Location	chr4:95572699-95572700
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:95568169..95569677-chr4:95571228..95573949,2	K562	blood:
2	chr4:95380787..95382998-chr4:95569911..95572847,2	K562	blood:
3	chr4:95569249..95571997-chr4:95572329..95574051,2	MCF-7	breast:
4	chr4:95566714..95569669-chr4:95570638..95572728,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10031423	0.83[EUR][1000 genomes]
rs1043853	0.81[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1048627	0.81[ASW][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1056773	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11097433	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11097434	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11097435	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11723532	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11724023	0.89[CEU][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs11725850	0.89[EUR][1000 genomes]
rs11732668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11732687	0.89[CEU][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs11734014	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12331240	0.81[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12331253	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12507763	0.81[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12511111	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12639887	0.82[CEU][hapmap]
rs12639980	0.84[EUR][1000 genomes]
rs12641023	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12643849	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12643867	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12649976	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs12650641	0.91[ASW][hapmap];0.80[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.85[LWK][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13110828	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13130496	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13135257	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs14082	0.81[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1472961	0.80[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1472962	0.81[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1472963	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1543013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2047025	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs2280002	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2902987	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34403066	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34438564	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34507709	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35959898	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3805263	0.84[CEU][hapmap]
rs3943	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4699567	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5013417	0.80[CEU][hapmap]
rs56921499	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60195134	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6532495	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6532496	0.91[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6532497	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6829381	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6839697	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs71601224	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7690296	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932216	chr4:95501261-96109807	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1003860	chr4:95507683-96120619	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv869528	chr4:95537649-96368018	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs951613	FAM190A	cis	cerebellum	SCAN
rs951613	ATOH1	cis	cerebellum	SCAN
rs951613	PDLIM5	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95493200-95584800	Weak transcription	Primary B cells from cord blood	blood
2	chr4:95525000-95586400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr4:95525000-95590000	Weak transcription	Lung	lung
4	chr4:95527800-95592200	Weak transcription	Pancreas	Pancrea
5	chr4:95533800-95594200	Weak transcription	Gastric	stomach
6	chr4:95537600-95573400	Weak transcription	Spleen	Spleen
7	chr4:95537600-95592800	Weak transcription	Fetal Stomach	stomach
8	chr4:95538000-95585200	Weak transcription	Colonic Mucosa	Colon
9	chr4:95538200-95582600	Weak transcription	Hela-S3	cervix
10	chr4:95538200-95586600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:95538600-95587000	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr4:95540000-95587000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr4:95540200-95597800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr4:95541200-95595600	Weak transcription	Primary T cells from cord blood	blood
15	chr4:95541400-95580200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr4:95543000-95586000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr4:95543000-95586400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr4:95547800-95573000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr4:95549000-95586600	Weak transcription	Brain Hippocampus Middle	brain
20	chr4:95555200-95578800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr4:95555200-95581800	Weak transcription	Ovary	ovary
22	chr4:95557200-95588600	Weak transcription	GM12878-XiMat	blood
23	chr4:95557400-95583800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr4:95557800-95586200	Weak transcription	Thymus	Thymus
25	chr4:95558200-95580800	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr4:95559000-95590200	Weak transcription	Right Ventricle	heart
27	chr4:95559600-95578200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr4:95561400-95585200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr4:95561600-95580200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr4:95562600-95578200	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr4:95563200-95584400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr4:95563600-95578200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:95563600-95578400	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr4:95563600-95583400	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr4:95563600-95589000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr4:95563800-95574200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr4:95563800-95579400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr4:95563800-95583400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr4:95563800-95583400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr4:95564000-95573600	Weak transcription	K562	blood
41	chr4:95564000-95578400	Weak transcription	NHEK	skin
42	chr4:95564000-95581200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr4:95564000-95587000	Weak transcription	NHLF	lung
44	chr4:95564000-95595000	Weak transcription	NHDF-Ad	bronchial
45	chr4:95567800-95582200	Weak transcription	Stomach Smooth Muscle	stomach
46	chr4:95567800-95587400	Weak transcription	HepG2	liver
47	chr4:95568200-95575200	Weak transcription	Adipose Nuclei	Adipose
48	chr4:95568200-95578200	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr4:95568400-95572800	Weak transcription	NH-A	brain
50	chr4:95568400-95575600	Weak transcription	Monocytes-CD14+_RO01746	blood

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