Variant report

Variant	rs3213940
Chromosome Location	chr5:61642937-61642938
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:61627722..61630548-chr5:61641622..61644001,2	MCF-7	breast:
2	chr5:61638389..61640483-chr5:61640496..61643629,3	K562	blood:
3	chr5:61635814..61638225-chr5:61640601..61643388,2	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1085103	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10939939	0.94[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11748930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11952777	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11957789	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12653369	0.86[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap]
rs12654228	0.87[EUR][1000 genomes]
rs12657535	0.86[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap]
rs12658601	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12659777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs152185	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs152189	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs152190	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs153872	0.89[EUR][1000 genomes]
rs15807	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs166006	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs166007	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs166008	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs166009	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs168847	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes]
rs16890606	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16890659	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs183729	0.89[EUR][1000 genomes]
rs185048	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs193682	0.89[EUR][1000 genomes]
rs247219	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs247224	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs247226	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs247236	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs247256	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs247263	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs247271	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs247272	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs247274	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs26612	0.95[CEU][hapmap];0.86[CHB][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs26633	0.95[CEU][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs27751	0.91[GIH][hapmap];0.85[TSI][hapmap]
rs32179	0.82[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap]
rs32182	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs35008	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35009	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35014	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35015	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35016	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs464058	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56095217	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57534920	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57835221	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58057332	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58266302	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59420453	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59629988	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60468842	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60803657	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62365304	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62374960	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62374961	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6449596	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6449597	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6864382	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6871913	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6882514	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs6886044	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6887181	0.85[EUR][1000 genomes]
rs6894270	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7704066	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7711530	0.87[CEU][hapmap]
rs7718580	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs784900	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs784901	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs784902	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[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
rs3213940	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	chr5:61603400-61658600	Weak transcription	Aorta	Aorta
2	chr5:61604400-61643800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr5:61604600-61658600	Weak transcription	Fetal Kidney	kidney
4	chr5:61607800-61669400	Weak transcription	NHLF	lung
5	chr5:61610200-61658600	Weak transcription	Ovary	ovary
6	chr5:61611600-61643800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr5:61612000-61661000	Weak transcription	Colon Smooth Muscle	Colon
8	chr5:61615600-61658600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:61618200-61647800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr5:61618400-61658600	Weak transcription	Hela-S3	cervix
11	chr5:61622400-61676000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:61622600-61643800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr5:61622600-61658800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr5:61623000-61643000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr5:61623000-61646200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr5:61623800-61643800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr5:61623800-61658600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr5:61624000-61669600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr5:61625400-61644000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr5:61625400-61646200	Weak transcription	Adipose Nuclei	Adipose
21	chr5:61628200-61644400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:61628800-61652000	Weak transcription	Fetal Brain Female	brain
23	chr5:61629200-61676400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr5:61629600-61645600	Weak transcription	HSMMtube	muscle
25	chr5:61629600-61665000	Weak transcription	Esophagus	oesophagus
26	chr5:61629800-61643200	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr5:61629800-61659400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr5:61630200-61646000	Weak transcription	Fetal Brain Male	brain
29	chr5:61630600-61643800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr5:61630600-61644000	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr5:61630800-61643600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:61631000-61644200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr5:61631000-61658400	Weak transcription	Colonic Mucosa	Colon
34	chr5:61631200-61643600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr5:61631200-61643800	Weak transcription	HSMM	muscle
36	chr5:61631200-61644000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:61631200-61644200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr5:61631200-61645800	Weak transcription	Brain Anterior Caudate	brain
39	chr5:61631200-61646000	Weak transcription	Fetal Muscle Trunk	muscle
40	chr5:61631200-61646200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr5:61631200-61646200	Weak transcription	Spleen	Spleen
42	chr5:61631200-61658800	Weak transcription	Pancreas	Pancrea
43	chr5:61631200-61669400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr5:61631200-61669600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr5:61631200-61676000	Weak transcription	Lung	lung
46	chr5:61631400-61643800	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr5:61631400-61645600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:61631400-61646000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr5:61631400-61646000	Weak transcription	Fetal Muscle Leg	muscle
50	chr5:61631400-61646200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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