Variant report

Variant	rs26638
Chromosome Location	chr5:61780582-61780583
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	chr5:61779738..61781733-chr5:61782229..61785139,2	MCF-7	breast:

Extended variants
information (count: 105 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10051492	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10051610	0.82[EUR][1000 genomes]
rs10053650	0.81[EUR][1000 genomes]
rs10065349	0.80[EUR][1000 genomes]
rs10078786	0.81[EUR][1000 genomes]
rs10461472	0.81[CEU][hapmap]
rs10471545	0.96[CEU][hapmap];0.91[CHB][hapmap]
rs10939939	0.85[CEU][hapmap]
rs12516160	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs12521329	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs13167856	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs13176954	0.81[EUR][1000 genomes]
rs13361143	0.81[CEU][hapmap]
rs1374009	0.91[YRI][hapmap]
rs152187	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs152188	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs152206	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs153856	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs153857	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs153858	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs153861	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs153862	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs153870	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16890622	0.81[CEU][hapmap]
rs173522	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs174647	0.81[CEU][hapmap]
rs181912	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1862569	0.81[EUR][1000 genomes]
rs190444	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2112982	0.81[EUR][1000 genomes]
rs2289883	0.84[CEU][hapmap]
rs2344396	0.96[CEU][hapmap];0.91[CHB][hapmap]
rs247228	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs247229	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs247234	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs247245	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs247247	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs247265	0.81[CEU][hapmap]
rs247270	0.84[CEU][hapmap]
rs255220	0.83[ASN][1000 genomes]
rs255390	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2591671	0.84[ASN][1000 genomes]
rs264530	0.84[CEU][hapmap]
rs26623	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26624	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26625	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26628	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs26629	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs26630	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs26645	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26649	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs27447	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs27542	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs32048	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32049	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32050	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs32051	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs32150	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs32154	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs32155	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs32158	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs32164	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs32166	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs32168	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs32171	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs32174	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs32181	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs32186	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs32187	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs32188	0.88[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35010	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35013	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35056	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35057	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35059	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35060	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs366238	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3822485	0.84[CEU][hapmap]
rs39923	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs39934	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs39935	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs40108	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4441833	0.81[CEU][hapmap]
rs4700012	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.83[EUR][1000 genomes]
rs4700498	0.80[EUR][1000 genomes]
rs4700499	0.81[EUR][1000 genomes]
rs706650	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7702634	0.81[CEU][hapmap]
rs7706610	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs7709562	0.81[EUR][1000 genomes]
rs7718484	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs7735107	0.82[EUR][1000 genomes]
rs9291762	0.91[YRI][hapmap]
rs959899	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024090	chr5:61258759-61921150	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1020255	chr5:61451792-62031365	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1027539	chr5:61457762-62000008	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1033578	chr5:61606610-61911153	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1025145	chr5:61624735-61824265	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1029708	chr5:61625813-61877628	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv881728	chr5:61630879-61857577	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv598348	chr5:61650843-61895124	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	esv35035	chr5:61657943-61792243	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv881729	chr5:61719506-61857577	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv881730	chr5:61750667-61883581	Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs26638	KIF2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61709800-61809200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr5:61728400-61807600	Weak transcription	Psoas Muscle	Psoas
3	chr5:61728800-61838200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr5:61730000-61834200	Weak transcription	Gastric	stomach
5	chr5:61732800-61805200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr5:61739200-61862800	Weak transcription	Brain Substantia Nigra	brain
7	chr5:61739600-61787800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr5:61744800-61838600	Weak transcription	Colonic Mucosa	Colon
9	chr5:61746200-61783600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr5:61748000-61794600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:61748000-61862800	Weak transcription	Right Ventricle	heart
12	chr5:61748600-61784400	Weak transcription	Lung	lung
13	chr5:61748600-61787000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:61749000-61786200	Weak transcription	Brain Anterior Caudate	brain
15	chr5:61750600-61785200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr5:61750600-61786000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr5:61757600-61792200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr5:61758800-61890000	Weak transcription	Small Intestine	intestine
19	chr5:61759000-61834200	Weak transcription	Esophagus	oesophagus
20	chr5:61759800-61790000	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr5:61760600-61781400	Weak transcription	Fetal Intestine Small	intestine
22	chr5:61760800-61847200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr5:61763400-61799400	Weak transcription	Fetal Heart	heart
24	chr5:61763800-61809600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr5:61764000-61833800	Weak transcription	Fetal Brain Female	brain
26	chr5:61764000-61858200	Weak transcription	Placenta	Placenta
27	chr5:61764200-61781200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr5:61764200-61781400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr5:61764200-61781400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr5:61764200-61784600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr5:61764200-61786200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr5:61764200-61786200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr5:61764200-61787000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr5:61764200-61794800	Weak transcription	Left Ventricle	heart
35	chr5:61764200-61796400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr5:61764200-61798800	Weak transcription	Spleen	Spleen
37	chr5:61764200-61818000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr5:61764200-61821200	Weak transcription	Aorta	Aorta
39	chr5:61764200-61826600	Weak transcription	Brain Hippocampus Middle	brain
40	chr5:61764200-61827000	Weak transcription	Thymus	Thymus
41	chr5:61764200-61830000	Weak transcription	Brain Angular Gyrus	brain
42	chr5:61764200-61895800	Weak transcription	Pancreas	Pancrea
43	chr5:61764400-61781200	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr5:61764400-61781600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr5:61764400-61792400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr5:61764400-61796600	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr5:61764400-61801200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr5:61764800-61786200	Weak transcription	Fetal Kidney	kidney
49	chr5:61765200-61793200	Weak transcription	Fetal Lung	lung
50	chr5:61765200-61794600	Weak transcription	HepG2	liver

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