Variant report

Variant	rs247263
Chromosome Location	chr5:61692515-61692516
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:61684151..61688740-chr5:61689725..61696494,7	K562	blood:
2	chr5:61687760..61696371-chr5:61696777..61701236,17	K562	blood:
3	chr5:61682102..61684562-chr5:61689312..61693081,3	K562	blood:
4	chr5:61682628..61684149-chr5:61691709..61694293,2	MCF-7	breast:
5	chr5:61691849..61694248-chr5:61708571..61710615,2	K562	blood:
6	chr5:61684677..61686970-chr5:61690927..61693209,3	K562	blood:
7	chr5:61687157..61690332-chr5:61692436..61695603,4	K562	blood:
8	chr5:61691955..61696371-chr5:61697756..61702688,14	K562	blood:

No data

Variant related genes	Relation type
ENSG00000086189	Chromatin interaction
ENSG00000086200	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1085103	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10939939	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11748930	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11952777	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11957789	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12654228	0.80[EUR][1000 genomes]
rs12658601	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12659777	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs152185	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs152189	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs152190	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs153872	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs15807	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs166006	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs166007	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs166008	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs166009	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs168847	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16890606	0.80[ASN][1000 genomes]
rs16890659	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs183729	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs185048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs193682	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs247219	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247224	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs247226	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs247256	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247271	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247272	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247274	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs26612	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3213940	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35008	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35009	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35014	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35015	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35016	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs464058	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56095217	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57534920	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57835221	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58057332	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58266302	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59420453	0.80[ASN][1000 genomes]
rs59629988	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60468842	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60803657	0.80[ASN][1000 genomes]
rs62365304	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62374960	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62374961	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6449596	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6449597	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6864382	0.82[ASN][1000 genomes]
rs6871913	0.80[ASN][1000 genomes]
rs6886044	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6894270	0.80[ASN][1000 genomes]
rs7704066	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7718580	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs784900	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs784901	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs784902	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	esv2757117	chr5:61649403-61748912	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
11	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
12	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs247263	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	chr5:61642400-61697400	Strong transcription	HUES64 Cell Line	embryonic stem cell
2	chr5:61642600-61696000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr5:61642600-61699200	Weak transcription	Gastric	stomach
4	chr5:61643000-61697000	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr5:61647600-61698000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:61656200-61698000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:61659800-61695800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr5:61661800-61698000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:61662000-61697800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr5:61662000-61697800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr5:61665400-61699000	Weak transcription	Esophagus	oesophagus
12	chr5:61666800-61698000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr5:61667000-61697200	Strong transcription	Primary B cells from peripheral blood	blood
14	chr5:61667400-61697200	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr5:61667600-61697800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:61667600-61698000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr5:61668000-61698000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:61668600-61697000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr5:61670000-61697200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:61672000-61698600	Weak transcription	Stomach Mucosa	stomach
21	chr5:61675000-61697800	Weak transcription	Small Intestine	intestine
22	chr5:61676800-61697800	Weak transcription	Right Atrium	heart
23	chr5:61676800-61699000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:61679600-61697000	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr5:61679600-61697600	Strong transcription	Liver	Liver
26	chr5:61680000-61696000	Strong transcription	HSMM	muscle
27	chr5:61680000-61697200	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr5:61680000-61697200	Strong transcription	Adipose Nuclei	Adipose
29	chr5:61680200-61694800	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr5:61680200-61696000	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr5:61680200-61697000	Strong transcription	Primary T cells from cord blood	blood
32	chr5:61680200-61697000	Strong transcription	Fetal Intestine Large	intestine
33	chr5:61680400-61697200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:61682000-61697000	Strong transcription	Placenta	Placenta
35	chr5:61682200-61699000	Weak transcription	Colonic Mucosa	Colon
36	chr5:61682800-61697800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr5:61683400-61697800	Weak transcription	Fetal Heart	heart
38	chr5:61683800-61697200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr5:61684000-61694800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:61684200-61698400	Strong transcription	Fetal Muscle Trunk	muscle
41	chr5:61684400-61693600	Strong transcription	Primary hematopoietic stem cells	blood
42	chr5:61685200-61696200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr5:61686200-61697000	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr5:61686800-61698200	Weak transcription	Fetal Brain Male	brain
45	chr5:61687400-61694600	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr5:61687400-61697200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr5:61687600-61697800	Weak transcription	Brain Substantia Nigra	brain
48	chr5:61688200-61693800	Weak transcription	Hela-S3	cervix
49	chr5:61688200-61698000	Strong transcription	Fetal Muscle Leg	muscle
50	chr5:61688400-61693600	Strong transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links