Variant report

Variant	rs12659777
Chromosome Location	chr5:61629159-61629160
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:61622009..61624604-chr5:61628091..61630897,2	K562	blood:
2	chr5:61601551..61603315-chr5:61628509..61630396,2	MCF-7	breast:
3	chr5:61601235..61603085-chr5:61628618..61631390,2	K562	blood:
4	chr5:61627722..61630548-chr5:61641622..61644001,2	MCF-7	breast:
5	chr5:61561395..61563266-chr5:61628626..61630582,2	K562	blood:

Variant related genes	Relation type
ENSG00000068796	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1085103	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10939939	0.94[CEU][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11748930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11952777	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11957789	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12653369	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes]
rs12654228	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12657535	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes]
rs12658601	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs152185	0.95[CEU][hapmap];0.85[CHB][hapmap];0.81[EUR][1000 genomes]
rs152189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs152190	0.89[EUR][1000 genomes]
rs153872	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs15807	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs166006	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs166007	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs166008	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs166009	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs168847	0.95[CEU][hapmap];0.86[CHB][hapmap]
rs16890606	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16890659	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs183729	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs185048	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs193682	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs247219	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs247224	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs247226	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs247236	0.95[CEU][hapmap];0.86[CHB][hapmap]
rs247256	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs247263	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs247271	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs247272	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs247274	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs26612	0.95[CEU][hapmap];0.85[CHB][hapmap];0.81[EUR][1000 genomes]
rs26633	0.95[CEU][hapmap]
rs3213940	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs32179	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs32182	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs35008	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35009	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35014	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35015	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs464058	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56095217	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57534920	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57835221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58057332	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58266302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59420453	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59629988	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60468842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60803657	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62365304	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62374960	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62374961	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449597	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6864382	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6871913	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6882514	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes]
rs6886044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6887181	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6894270	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6898615	0.82[AMR][1000 genomes]
rs7704066	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7711530	0.87[CEU][hapmap]
rs7718580	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs784900	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs784901	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs784902	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12659777	KIF2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61603200-61629200	Weak transcription	Lung	lung
2	chr5:61603200-61629200	Weak transcription	Spleen	Spleen
3	chr5:61603400-61658600	Weak transcription	Aorta	Aorta
4	chr5:61603600-61629200	Weak transcription	Psoas Muscle	Psoas
5	chr5:61603800-61629200	Weak transcription	Left Ventricle	heart
6	chr5:61604400-61629200	Weak transcription	Esophagus	oesophagus
7	chr5:61604400-61629400	Weak transcription	Pancreas	Pancrea
8	chr5:61604400-61643800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr5:61604600-61630000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr5:61604600-61658600	Weak transcription	Fetal Kidney	kidney
11	chr5:61606800-61629400	Weak transcription	Fetal Thymus	thymus
12	chr5:61607200-61629200	Weak transcription	HSMMtube	muscle
13	chr5:61607800-61669400	Weak transcription	NHLF	lung
14	chr5:61610200-61658600	Weak transcription	Ovary	ovary
15	chr5:61610400-61629400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:61611400-61629200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:61611600-61630200	Weak transcription	Fetal Intestine Large	intestine
18	chr5:61611600-61639000	Weak transcription	HMEC	breast
19	chr5:61611600-61643800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr5:61611800-61630000	Weak transcription	NHEK	skin
21	chr5:61612000-61642400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr5:61612000-61661000	Weak transcription	Colon Smooth Muscle	Colon
23	chr5:61615600-61629200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:61615600-61658600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr5:61618000-61629200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr5:61618000-61629200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:61618000-61629400	Weak transcription	Fetal Stomach	stomach
28	chr5:61618200-61629600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr5:61618200-61647800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr5:61618400-61629200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr5:61618400-61658600	Weak transcription	Hela-S3	cervix
32	chr5:61618600-61629400	Weak transcription	Placenta	Placenta
33	chr5:61619200-61630000	Weak transcription	Colonic Mucosa	Colon
34	chr5:61620200-61629200	Enhancers	Brain Substantia Nigra	brain
35	chr5:61621600-61629200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr5:61621600-61631600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr5:61621800-61638000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr5:61622400-61633400	Weak transcription	HUVEC	blood vessel
39	chr5:61622400-61676000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:61622600-61629200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr5:61622600-61643800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr5:61622600-61658800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr5:61623000-61643000	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr5:61623000-61646200	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr5:61623400-61629200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr5:61623800-61629200	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr5:61623800-61643800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr5:61623800-61658600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr5:61624000-61669600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr5:61625400-61644000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links