Variant report

Variant	rs35238667
Chromosome Location	chr5:61680407-61680408
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:61680086..61685494-chr5:61685831..61690801,7	MCF-7	breast:
2	chr5:61680177..61684134-chr5:61684359..61686623,3	K562	blood:
3	chr5:61679991..61682016-chr5:61697548..61699312,2	MCF-7	breast:
4	chr5:61677896..61680511-chr5:61698286..61699795,2	K562	blood:

Variant related genes	Relation type
ENSG00000086189	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1108158	0.83[ASN][1000 genomes]
rs11740652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11742167	0.80[ASN][1000 genomes]
rs11747516	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12655562	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13155253	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13156073	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13156695	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13163533	0.83[EUR][1000 genomes]
rs13169321	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13170425	0.83[ASN][1000 genomes]
rs13174779	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13176923	0.80[ASN][1000 genomes]
rs13178729	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13189446	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13190153	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs153864	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs16875037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890613	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16890618	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890628	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890634	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890651	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2059162	0.83[ASN][1000 genomes]
rs2063255	0.83[ASN][1000 genomes]
rs2272291	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs246198	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs27090	0.80[ASN][1000 genomes]
rs34220654	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34596001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35054	0.82[EUR][1000 genomes]
rs35055	0.82[EUR][1000 genomes]
rs35311093	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35572300	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35699711	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35744020	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35746052	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35794032	0.83[ASN][1000 genomes]
rs35808056	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35815430	0.96[EUR][1000 genomes]
rs35842742	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36105063	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3776612	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3776614	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs417822	0.82[EUR][1000 genomes]
rs4289514	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71617426	1.00[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs71617427	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71617428	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71617429	0.84[EUR][1000 genomes]
rs7446543	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs971965	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
rs35238667	KIF2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61639800-61684200	Weak transcription	Psoas Muscle	Psoas
2	chr5:61641400-61682400	Weak transcription	Fetal Heart	heart
3	chr5:61642400-61697400	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr5:61642600-61688400	Weak transcription	Right Ventricle	heart
5	chr5:61642600-61696000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr5:61642600-61699200	Weak transcription	Gastric	stomach
7	chr5:61643000-61697000	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr5:61643800-61680600	Strong transcription	Placenta	Placenta
9	chr5:61644000-61689000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr5:61645400-61689200	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr5:61647000-61690000	Weak transcription	Spleen	Spleen
12	chr5:61647600-61698000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr5:61656200-61698000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:61656800-61687800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:61658400-61691800	Strong transcription	Dnd41	blood
16	chr5:61659800-61695800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:61661800-61698000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr5:61662000-61697800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr5:61662000-61697800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr5:61664600-61689200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr5:61665400-61699000	Weak transcription	Esophagus	oesophagus
22	chr5:61665600-61688000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr5:61666800-61698000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr5:61667000-61691200	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr5:61667000-61691600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr5:61667000-61697200	Strong transcription	Primary B cells from peripheral blood	blood
27	chr5:61667400-61697200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr5:61667600-61697800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:61667600-61698000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr5:61667800-61681400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr5:61668000-61698000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr5:61668400-61685600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr5:61668600-61697000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr5:61669200-61690200	Strong transcription	HUVEC	blood vessel
35	chr5:61669400-61680800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:61669400-61681600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:61669400-61682600	Strong transcription	Thymus	Thymus
38	chr5:61669400-61683000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr5:61669400-61683400	Strong transcription	Fetal Muscle Trunk	muscle
40	chr5:61669400-61685800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
41	chr5:61669400-61690800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr5:61669600-61685000	Strong transcription	Fetal Brain Female	brain
43	chr5:61669600-61687600	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr5:61670000-61697200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr5:61670800-61690000	Weak transcription	Aorta	Aorta
46	chr5:61672000-61698600	Weak transcription	Stomach Mucosa	stomach
47	chr5:61672200-61680600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr5:61673800-61682600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr5:61674200-61682000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr5:61674200-61683200	Strong transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links