Variant report

Variant	rs10801192
Chromosome Location	chr1:193253160-193253161
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:193253060..193255508-chr1:193274779..193276360,2	MCF-7	breast:
2	chr1:193251220..193253258-chr1:193254236..193256682,2	K562	blood:

Extended variants
information (count: 139 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs10399607	0.86[ASN][1000 genomes]
rs10399929	0.86[ASN][1000 genomes]
rs10494674	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs10732293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10733078	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap]
rs10737620	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10737621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10737622	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10737623	1.00[ASN][1000 genomes]
rs10754044	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10754047	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10754048	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10754049	1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs10754052	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10754053	0.84[ASN][1000 genomes]
rs10754054	0.95[ASN][1000 genomes]
rs10754055	1.00[ASN][1000 genomes]
rs10801173	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs10801174	1.00[CEU][hapmap]
rs10801177	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs10801178	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs10801179	1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs10801183	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10801184	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs10801187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10801188	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10801189	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10801190	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10801191	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10801194	0.82[ASN][1000 genomes]
rs10921312	1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs10921318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10921323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10921325	0.85[GIH][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10921326	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10921328	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10921330	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10921334	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10921336	0.97[ASN][1000 genomes]
rs11577299	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap]
rs12047390	0.82[CHB][hapmap]
rs12064521	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12078145	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12090626	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap]
rs12124282	0.90[EUR][1000 genomes]
rs12126529	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs12145057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1221502	0.80[ASN][1000 genomes]
rs12410213	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1325197	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1361404	0.87[CEU][hapmap];0.82[CHB][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs1361405	0.82[CHB][hapmap]
rs1408830	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1416977	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1536097	0.84[ASN][1000 genomes]
rs1536098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1536099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1539724	0.91[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap]
rs1578242	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1578243	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1616234	0.82[ASN][1000 genomes]
rs1632444	1.00[ASN][1000 genomes]
rs1749424	0.99[ASN][1000 genomes]
rs1770000	0.88[EUR][1000 genomes]
rs2078083	0.93[ASN][1000 genomes]
rs2181408	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs2182106	1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2186016	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs2251699	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2254646	0.99[ASN][1000 genomes]
rs2370029	1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs2477549	0.81[ASN][1000 genomes]
rs2486842	0.92[ASN][1000 genomes]
rs2486843	0.89[EUR][1000 genomes]
rs3738244	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3806351	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs4379660	1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4450000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs4466634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs4657744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs4657747	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4657843	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs4657847	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap]
rs4657848	1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs474328	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs475163	0.97[ASN][1000 genomes]
rs503265	0.99[ASN][1000 genomes]
rs523402	0.81[ASN][1000 genomes]
rs524701	0.97[ASN][1000 genomes]
rs531327	0.90[EUR][1000 genomes]
rs543788	1.00[ASN][1000 genomes]
rs569656	0.95[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs571029	1.00[ASN][1000 genomes]
rs578639	0.80[ASN][1000 genomes]
rs6428152	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs6428153	0.85[ASN][1000 genomes]
rs6428154	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6428155	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6428156	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6428157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6428159	1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6428160	0.97[ASN][1000 genomes]
rs6662104	0.85[EUR][1000 genomes]
rs6663162	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6665069	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs6665666	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6671237	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs6671476	1.00[ASN][1000 genomes]
rs6673271	1.00[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs6675827	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6675833	1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6676878	1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6680224	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6689006	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6697079	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6702762	0.85[EUR][1000 genomes]
rs693519	0.95[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs7514072	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap]
rs7515024	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7518792	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7519242	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs7534504	0.80[EUR][1000 genomes]
rs7543029	0.85[EUR][1000 genomes]
rs7545223	0.86[ASN][1000 genomes]
rs7546869	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7547615	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap]
rs7554925	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs817136	0.97[ASN][1000 genomes]
rs817138	0.81[ASN][1000 genomes]
rs817140	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs843844	0.95[CHB][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs912070	1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs912071	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs942680	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9783104	1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs9887974	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[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	nsv832148	chr1:193143945-193292897	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv872831	chr1:193152317-193322087	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1001174	chr1:193186758-193363372	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10801192	CDC73	cis	cerebellum	SCAN
rs10801192	GLRX2	cis	parietal	SCAN
rs10801192	B3GALT2	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:193218600-193258200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:193222400-193253800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:193229000-193254800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:193239800-193254600	Weak transcription	HSMM	muscle
5	chr1:193243800-193254400	Weak transcription	HSMMtube	muscle
6	chr1:193243800-193267800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:193245400-193253200	Weak transcription	Primary T cells from cord blood	blood
8	chr1:193250200-193257800	Weak transcription	NHDF-Ad	bronchial
9	chr1:193252600-193254000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr1:193252600-193254000	Enhancers	Fetal Thymus	thymus
11	chr1:193252600-193254600	Weak transcription	NHLF	lung
12	chr1:193252600-193254800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:193252600-193256400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:193252600-193258000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr1:193252800-193253200	Enhancers	Pancreas	Pancrea
16	chr1:193252800-193254000	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr1:193252800-193254200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:193252800-193254800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:193252800-193258000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:193253000-193253600	Enhancers	Thymus	Thymus

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