Variant report

Variant	rs10801173
Chromosome Location	chr1:193054485-193054486
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:193036534..193039391-chr1:193053045..193055272,2	K562	blood:
2	chr1:193021502..193024207-chr1:193053848..193055702,2	K562	blood:
3	chr1:193054112..193056776-chr1:193063002..193065474,2	K562	blood:
4	chr1:193051806..193058060-chr1:193058254..193062557,7	K562	blood:
5	chr1:193046427..193048630-chr1:193054285..193055825,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116747	Chromatin interaction
ENSG00000272579	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10494674	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10732293	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10733078	0.81[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10737620	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.99[ASN][1000 genomes]
rs10737621	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10737622	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10754044	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10754046	0.85[ASN][1000 genomes]
rs10754047	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10754048	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10754049	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10754052	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs10801167	0.93[ASN][1000 genomes]
rs10801174	0.92[CEU][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10801175	0.94[ASN][1000 genomes]
rs10801177	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.85[ASN][1000 genomes]
rs10801178	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10801179	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10801180	0.83[ASN][1000 genomes]
rs10801182	0.83[ASN][1000 genomes]
rs10801183	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10801184	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.82[ASN][1000 genomes]
rs10801187	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs10801189	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.93[YRI][hapmap]
rs10921304	0.84[ASN][1000 genomes]
rs10921305	0.92[ASN][1000 genomes]
rs10921308	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10921309	0.81[CHD][hapmap]
rs10921310	0.96[ASN][1000 genomes]
rs10921312	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10921313	0.96[ASN][1000 genomes]
rs10921317	0.85[ASN][1000 genomes]
rs10921318	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs10921319	0.84[ASN][1000 genomes]
rs10921323	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs10921325	0.90[JPT][hapmap]
rs10921326	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs10921330	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11577299	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.93[YRI][hapmap];0.83[ASN][1000 genomes]
rs11583763	0.93[ASN][1000 genomes]
rs12086884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[ASN][1000 genomes]
rs12090626	0.83[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs12126529	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12137318	0.84[ASN][1000 genomes]
rs12141392	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12145057	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[ASN][1000 genomes]
rs12410213	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12735445	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1325197	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs1408830	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs1536098	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1536099	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs1539724	0.82[CEU][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs1555555	0.96[ASN][1000 genomes]
rs1890660	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.97[MKK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2181408	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2182106	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs2186016	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.84[ASN][1000 genomes]
rs2275444	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[ASN][1000 genomes]
rs2370028	0.84[ASN][1000 genomes]
rs2370029	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2370079	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2370081	0.93[ASN][1000 genomes]
rs3738244	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3753948	0.97[ASN][1000 genomes]
rs3806351	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.83[YRI][hapmap];0.87[ASN][1000 genomes]
rs3818865	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3820417	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3945872	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4379660	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs4450000	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[ASN][1000 genomes]
rs4466634	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4657744	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4657745	0.83[ASN][1000 genomes]
rs4657840	0.93[ASN][1000 genomes]
rs4657842	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4657843	1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4657845	0.96[ASN][1000 genomes]
rs4657846	0.87[ASN][1000 genomes]
rs4657847	0.81[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs4657848	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs4658079	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6428151	0.85[ASN][1000 genomes]
rs6428152	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6428154	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6428156	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs6428157	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs6428159	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6661522	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs6663431	1.00[ASN][1000 genomes]
rs6665069	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6665666	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6671237	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6672649	0.92[ASN][1000 genomes]
rs6673271	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6675833	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6676322	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[ASN][1000 genomes]
rs6676416	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs6676878	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6680224	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs6692342	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6692805	0.93[ASN][1000 genomes]
rs6697079	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap]
rs6703727	0.96[ASN][1000 genomes]
rs7514072	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.93[YRI][hapmap];0.84[ASN][1000 genomes]
rs7515024	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs7518792	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs7519242	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7534257	0.90[ASN][1000 genomes]
rs7542466	0.88[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];0.97[MKK][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7547615	0.81[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7553247	0.99[ASN][1000 genomes]
rs912070	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs912071	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9427838	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9783104	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532618	chr1:192537006-193149179	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv1002094	chr1:192968080-193084045	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10801173	GLRX2	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:193033200-193067600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:193044000-193055800	Strong transcription	Fetal Lung	lung
3	chr1:193044800-193056000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr1:193044800-193061200	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:193045000-193054600	Strong transcription	Placenta	Placenta
6	chr1:193045000-193055200	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:193045000-193055400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:193045000-193055600	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:193045000-193055800	Strong transcription	Primary T helper cells PMA-I stimulated	--
10	chr1:193045200-193055200	Strong transcription	HSMM	muscle
11	chr1:193045200-193070200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:193045400-193055600	Strong transcription	NH-A	brain
13	chr1:193045400-193056800	Strong transcription	NHDF-Ad	bronchial
14	chr1:193045600-193054800	Strong transcription	Fetal Thymus	thymus
15	chr1:193045800-193055400	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr1:193045800-193055600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:193045800-193055800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:193045800-193055800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:193045800-193055800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:193045800-193056000	Strong transcription	Dnd41	blood
21	chr1:193045800-193056200	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr1:193046000-193055200	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr1:193046000-193055600	Strong transcription	Primary B cells from peripheral blood	blood
24	chr1:193046000-193056000	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr1:193046400-193055600	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr1:193046400-193055600	Strong transcription	Colon Smooth Muscle	Colon
27	chr1:193046400-193055600	Strong transcription	HUVEC	blood vessel
28	chr1:193046400-193056200	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr1:193046800-193070400	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr1:193047000-193055400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr1:193047000-193059000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr1:193047000-193062600	Weak transcription	Small Intestine	intestine
33	chr1:193047000-193066000	Weak transcription	Right Ventricle	heart
34	chr1:193047400-193071400	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr1:193047600-193054800	Strong transcription	Primary hematopoietic stem cells	blood
36	chr1:193047600-193054800	Strong transcription	Liver	Liver
37	chr1:193047600-193056800	Strong transcription	Osteobl	bone
38	chr1:193047600-193059200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr1:193047800-193054600	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr1:193047800-193054800	Strong transcription	Duodenum Mucosa	Duodenum
41	chr1:193047800-193055600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:193048200-193056200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:193048200-193056600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:193048200-193072600	Weak transcription	Stomach Mucosa	stomach
45	chr1:193048400-193055600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:193048600-193055000	Strong transcription	Brain Germinal Matrix	brain
47	chr1:193048600-193073000	Weak transcription	Fetal Brain Male	brain
48	chr1:193048800-193055600	Strong transcription	K562	blood
49	chr1:193048800-193070000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:193049000-193054600	Strong transcription	HMEC	breast

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