Variant report

Variant	rs10939939
Chromosome Location	chr5:61648738-61648739
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:61601612..61603523-chr5:61647478..61650855,3	MCF-7	breast:
2	chr5:61645079..61646734-chr5:61646742..61649036,2	K562	blood:
3	chr5:61604639..61607587-chr5:61647579..61650088,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068796	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10471545	0.89[CEU][hapmap]
rs1085103	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11748930	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11952777	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11957789	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12654228	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12658601	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12659777	0.94[CEU][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs152185	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs152187	0.83[CEU][hapmap]
rs152189	0.94[CEU][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs152190	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs153857	0.83[CEU][hapmap]
rs153858	0.83[CEU][hapmap]
rs153862	0.83[CEU][hapmap]
rs153872	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs15807	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs166006	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs166007	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs166008	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs166009	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs168847	0.89[CEU][hapmap];0.81[AMR][1000 genomes]
rs16890606	0.89[CEU][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16890659	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs173522	0.83[CEU][hapmap]
rs183729	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs185048	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs193682	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2344396	0.89[CEU][hapmap]
rs247219	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247224	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs247226	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs247229	0.83[CEU][hapmap]
rs247236	0.89[CEU][hapmap]
rs247245	0.83[CEU][hapmap]
rs247256	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247263	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247271	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247272	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247274	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs26612	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs26624	0.83[CEU][hapmap]
rs26630	0.83[CEU][hapmap]
rs26633	0.89[CEU][hapmap]
rs26638	0.85[CEU][hapmap]
rs26645	0.83[CEU][hapmap]
rs27542	0.83[CEU][hapmap]
rs3213940	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs32182	0.83[CEU][hapmap]
rs35008	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35009	0.94[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35010	0.83[CEU][hapmap]
rs35014	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35015	0.94[CEU][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35016	0.94[CEU][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35059	0.83[CEU][hapmap]
rs464058	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56095217	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57534920	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57835221	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58057332	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58266302	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59420453	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59629988	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60468842	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60803657	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62365304	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62374960	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62374961	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6449596	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6449597	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6864382	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6871913	0.83[CEU][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6882514	0.83[CEU][hapmap]
rs6886044	0.94[CEU][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6887181	0.82[EUR][1000 genomes]
rs6894270	0.83[CEU][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7704066	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7718580	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs784900	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs784901	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs784902	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	esv2757996	chr5:61403138-61687817	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2759345	chr5:61403138-61748912	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv881726	chr5:61556730-61676911	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	nsv881727	chr5:61578041-61700970	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	23 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10939939	KIF2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61603400-61658600	Weak transcription	Aorta	Aorta
2	chr5:61604600-61658600	Weak transcription	Fetal Kidney	kidney
3	chr5:61607800-61669400	Weak transcription	NHLF	lung
4	chr5:61610200-61658600	Weak transcription	Ovary	ovary
5	chr5:61612000-61661000	Weak transcription	Colon Smooth Muscle	Colon
6	chr5:61615600-61658600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:61618400-61658600	Weak transcription	Hela-S3	cervix
8	chr5:61622400-61676000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:61622600-61658800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr5:61623800-61658600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr5:61624000-61669600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr5:61628800-61652000	Weak transcription	Fetal Brain Female	brain
13	chr5:61629200-61676400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr5:61629600-61665000	Weak transcription	Esophagus	oesophagus
15	chr5:61629800-61659400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr5:61631000-61658400	Weak transcription	Colonic Mucosa	Colon
17	chr5:61631200-61658800	Weak transcription	Pancreas	Pancrea
18	chr5:61631200-61669400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:61631200-61669600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr5:61631200-61676000	Weak transcription	Lung	lung
21	chr5:61631400-61660000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:61632400-61650400	Weak transcription	A549	lung
23	chr5:61635000-61650600	Weak transcription	Brain Germinal Matrix	brain
24	chr5:61635200-61651800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr5:61637000-61649600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr5:61638600-61671200	Weak transcription	Small Intestine	intestine
27	chr5:61639600-61658600	Weak transcription	Brain Hippocampus Middle	brain
28	chr5:61639800-61651200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr5:61639800-61684200	Weak transcription	Psoas Muscle	Psoas
30	chr5:61641200-61657200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr5:61641400-61658600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr5:61641400-61682400	Weak transcription	Fetal Heart	heart
33	chr5:61642200-61649400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr5:61642400-61665400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr5:61642400-61697400	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr5:61642600-61656000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr5:61642600-61660800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:61642600-61688400	Weak transcription	Right Ventricle	heart
39	chr5:61642600-61696000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr5:61642600-61699200	Weak transcription	Gastric	stomach
41	chr5:61642800-61654000	Weak transcription	Brain Substantia Nigra	brain
42	chr5:61642800-61659000	Weak transcription	HepG2	liver
43	chr5:61643000-61650600	Weak transcription	NHEK	skin
44	chr5:61643000-61657600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr5:61643000-61658600	Weak transcription	Brain Angular Gyrus	brain
46	chr5:61643000-61658600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr5:61643000-61660400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr5:61643000-61697000	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr5:61643200-61650000	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr5:61643400-61649800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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