Variant report

Variant	rs2359173
Chromosome Location	chr1:114196495-114196496
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:114192533..114195084-chr1:114195478..114197038,2	K562	blood:
2	chr1:114194523..114197911-chr1:114198408..114201889,3	K562	blood:
3	chr1:114191701..114193455-chr1:114196104..114197721,2	MCF-7	breast:
4	chr1:114183983..114185528-chr1:114194793..114196565,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10127930	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10489936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1080307	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];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1217384	0.82[EUR][1000 genomes]
rs12723023	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12729708	0.82[EUR][1000 genomes]
rs12730675	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12730735	0.87[EUR][1000 genomes]
rs12731010	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12731969	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12734625	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12735104	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12739970	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12746609	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12748727	0.88[EUR][1000 genomes]
rs12752932	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12753075	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12753351	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12758546	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12760457	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs13374352	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17274550	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17274620	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17274634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17359302	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17462614	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17508163	0.84[ASN][1000 genomes]
rs17508814	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17509390	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1885454	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2040040	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2359174	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34042871	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34258372	0.91[CEU][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34341173	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34649199	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34698891	0.92[EUR][1000 genomes]
rs34799402	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs34857922	0.82[EUR][1000 genomes]
rs34877889	0.87[EUR][1000 genomes]
rs35320278	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35383900	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35836713	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36115604	0.88[EUR][1000 genomes]
rs3747998	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3748003	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752953	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs3761931	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[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];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3789595	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3789599	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap]
rs3789607	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3789609	0.87[EUR][1000 genomes]
rs4581284	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs55855422	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs56257513	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61817579	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61817586	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61817617	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61819423	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61819424	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61820162	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6668829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6674848	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66782936	0.87[ASN][1000 genomes]
rs6703387	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7533391	0.82[EUR][1000 genomes]
rs7533605	0.88[EUR][1000 genomes]
rs7549685	0.86[EUR][1000 genomes]
rs7555354	0.88[EUR][1000 genomes]
rs9803891	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[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	nsv1012324	chr1:114135133-114206843	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv872161	chr1:114162194-114280135	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2359173	CD58	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114161800-114199800	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:114171600-114241400	Weak transcription	Right Ventricle	heart
3	chr1:114173000-114214400	Weak transcription	Esophagus	oesophagus
4	chr1:114173000-114226800	Weak transcription	Aorta	Aorta
5	chr1:114173600-114206000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:114173800-114199600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr1:114173800-114201800	Weak transcription	Colonic Mucosa	Colon
8	chr1:114173800-114201800	Weak transcription	Lung	lung
9	chr1:114173800-114214400	Weak transcription	Pancreas	Pancrea
10	chr1:114173800-114236000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:114179800-114239600	Weak transcription	Spleen	Spleen
12	chr1:114181200-114199400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:114181800-114199800	Weak transcription	Fetal Brain Female	brain
14	chr1:114182000-114219600	Weak transcription	Fetal Kidney	kidney
15	chr1:114182200-114197600	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:114182600-114206200	Weak transcription	Hela-S3	cervix
17	chr1:114182800-114201800	Weak transcription	Brain Germinal Matrix	brain
18	chr1:114182800-114201800	Weak transcription	Fetal Brain Male	brain
19	chr1:114182800-114217400	Weak transcription	NHDF-Ad	bronchial
20	chr1:114183000-114200000	Weak transcription	HSMMtube	muscle
21	chr1:114183000-114201200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:114183000-114235800	Weak transcription	Dnd41	blood
23	chr1:114183200-114199600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:114183400-114199800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:114183400-114215800	Weak transcription	Fetal Lung	lung
26	chr1:114183600-114199200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:114183600-114216400	Weak transcription	A549	lung
28	chr1:114184400-114199600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:114184600-114204800	Weak transcription	Psoas Muscle	Psoas
30	chr1:114184800-114199800	Weak transcription	Brain Anterior Caudate	brain
31	chr1:114184800-114201800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:114185000-114199600	Weak transcription	Brain Substantia Nigra	brain
33	chr1:114185200-114199400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr1:114185200-114224400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:114185400-114200400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:114185400-114201200	Weak transcription	Brain Angular Gyrus	brain
37	chr1:114185400-114214600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:114185400-114228000	Weak transcription	HepG2	liver
39	chr1:114185800-114223600	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:114186800-114200000	Weak transcription	Fetal Muscle Leg	muscle
41	chr1:114187400-114201800	Weak transcription	Primary T cells from cord blood	blood
42	chr1:114187600-114196800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:114188200-114201800	Weak transcription	Small Intestine	intestine
44	chr1:114188200-114202800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:114189000-114197200	Strong transcription	Liver	Liver
46	chr1:114190000-114199400	Weak transcription	Fetal Heart	heart
47	chr1:114190000-114201800	Weak transcription	NH-A	brain
48	chr1:114190000-114206200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:114190000-114217600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:114190000-114220000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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