Variant report

Variant	rs17274634
Chromosome Location	chr1:114217527-114217528
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	chr1:113930366..113932771-chr1:114217459..114219362,2	MCF-7	breast:
2	chr1:113931113..113934669-chr1:114216801..114220484,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000081026	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10127930	0.89[EUR][1000 genomes]
rs10489936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1080307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1217384	0.82[EUR][1000 genomes]
rs12723023	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12729708	0.82[EUR][1000 genomes]
rs12730675	0.84[ASN][1000 genomes]
rs12730735	0.87[EUR][1000 genomes]
rs12731010	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12731969	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12734625	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12735104	0.88[EUR][1000 genomes]
rs12739970	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12746609	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12748727	0.88[EUR][1000 genomes]
rs12752932	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12753075	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12753351	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12758546	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12760457	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];0.88[EUR][1000 genomes]
rs13374352	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17274550	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17274620	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17359302	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17462614	0.92[EUR][1000 genomes]
rs17508163	0.82[ASN][1000 genomes]
rs17508814	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17509390	0.88[EUR][1000 genomes]
rs1885454	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]
rs2040040	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];0.89[EUR][1000 genomes]
rs2359173	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]
rs2359174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[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]
rs34042871	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[ASN][1000 genomes]
rs34341173	0.89[EUR][1000 genomes]
rs34649199	0.89[EUR][1000 genomes]
rs34698891	0.92[EUR][1000 genomes]
rs34799402	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs34857922	0.82[EUR][1000 genomes]
rs34877889	0.87[EUR][1000 genomes]
rs35320278	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35383900	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35836713	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36115604	0.88[EUR][1000 genomes]
rs3747998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3748003	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]
rs3752953	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs3761931	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3789595	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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[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];0.88[EUR][1000 genomes]
rs3789609	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs4581284	0.84[ASN][1000 genomes]
rs55855422	0.84[ASN][1000 genomes]
rs56257513	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61817579	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61817586	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61817617	0.89[EUR][1000 genomes]
rs61819423	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61819424	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61820162	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6668829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs6674848	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66782936	0.84[ASN][1000 genomes]
rs6696459	0.91[YRI][hapmap]
rs6703387	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];0.88[EUR][1000 genomes]
rs7512645	1.00[YRI][hapmap];0.80[AFR][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];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[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	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
2	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
rs17274634	CD58	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114171600-114241400	Weak transcription	Right Ventricle	heart
2	chr1:114173000-114226800	Weak transcription	Aorta	Aorta
3	chr1:114173800-114236000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:114179800-114239600	Weak transcription	Spleen	Spleen
5	chr1:114182000-114219600	Weak transcription	Fetal Kidney	kidney
6	chr1:114183000-114235800	Weak transcription	Dnd41	blood
7	chr1:114185200-114224400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:114185400-114228000	Weak transcription	HepG2	liver
9	chr1:114185800-114223600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:114190000-114217600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:114190000-114220000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:114194000-114223600	Weak transcription	Left Ventricle	heart
13	chr1:114196600-114226400	Weak transcription	Gastric	stomach
14	chr1:114200200-114227800	Weak transcription	Stomach Mucosa	stomach
15	chr1:114201600-114219400	Weak transcription	Fetal Heart	heart
16	chr1:114202000-114241400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:114202400-114220000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:114203000-114232000	Weak transcription	Fetal Brain Female	brain
19	chr1:114203000-114237800	Weak transcription	NH-A	brain
20	chr1:114203200-114224800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:114203200-114232200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:114203200-114237600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:114203200-114298600	Weak transcription	Fetal Brain Male	brain
24	chr1:114203400-114237800	Weak transcription	Brain Angular Gyrus	brain
25	chr1:114205000-114219800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:114206600-114223600	Weak transcription	Hela-S3	cervix
27	chr1:114206600-114226400	Weak transcription	NHLF	lung
28	chr1:114206600-114229800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:114207000-114220000	Weak transcription	HSMM	muscle
30	chr1:114207200-114218000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:114207200-114220000	Weak transcription	HSMMtube	muscle
32	chr1:114207400-114230600	Weak transcription	NHEK	skin
33	chr1:114209600-114229600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:114209800-114232400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr1:114211200-114231400	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr1:114211600-114234600	Weak transcription	Brain Germinal Matrix	brain
37	chr1:114212000-114219800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr1:114213000-114221800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:114213400-114225400	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr1:114213600-114218400	Strong transcription	Liver	Liver
41	chr1:114213600-114232000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:114213600-114241600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:114213800-114217800	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr1:114214000-114218600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:114214200-114217800	Strong transcription	Fetal Stomach	stomach
46	chr1:114214400-114220000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr1:114214800-114218200	Strong transcription	Fetal Intestine Large	intestine
48	chr1:114214800-114232400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:114215000-114226800	Weak transcription	Ovary	ovary
50	chr1:114215400-114235800	Weak transcription	Esophagus	oesophagus

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