Variant report

Variant	rs16890613
Chromosome Location	chr5:61582463-61582464
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:61581288..61583777-chr5:61597562..61600246,2	K562	blood:
2	chr5:61570576..61576152-chr5:61577980..61582631,7	K562	blood:
3	chr5:61558370..61559977-chr5:61580738..61582579,2	K562	blood:
4	chr5:61581120..61583166-chr5:61590441..61591948,2	MCF-7	breast:
5	chr5:61582450..61585582-chr5:61601200..61603470,3	MCF-7	breast:
6	chr5:61580058..61581807-chr5:61582180..61584252,2	K562	blood:
7	chr5:61579949..61585428-chr5:61600379..61606921,7	K562	blood:

Variant related genes	Relation type
ENSG00000068796	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1108158	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11740652	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11742167	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11747516	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11750109	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12655562	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13155253	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13156073	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13156695	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13161789	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13162519	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13162821	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13169321	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13170425	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13174779	0.89[ASN][1000 genomes]
rs13176923	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13178729	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13181377	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13189446	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs153860	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs153864	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs153866	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs153869	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs153873	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs16875037	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16890618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16890628	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16890634	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16890651	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16898838	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17382217	1.00[CEU][hapmap]
rs2059162	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2063255	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2272291	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2441115	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs27090	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs34220654	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34596001	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35011	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs35012	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs35058	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs35238667	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35311093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35572300	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35672643	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35699711	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35744020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35746052	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35794032	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35808056	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35815430	0.83[EUR][1000 genomes]
rs35842742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36105063	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3776612	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3776614	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3822487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4289514	0.89[ASN][1000 genomes]
rs71617425	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71617426	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71617427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71617428	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7446543	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs814169	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs971965	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv830318	chr5:61415713-61623320	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	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
6	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
7	esv2755585	chr5:61535831-61618595	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	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
9	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16890613	KIF2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61579400-61583000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr5:61580200-61582800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr5:61580400-61582800	Weak transcription	Fetal Intestine Large	intestine
4	chr5:61580400-61585000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr5:61580600-61582800	Weak transcription	Placenta	Placenta
6	chr5:61581000-61583400	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr5:61581000-61584200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr5:61581200-61583000	Weak transcription	Primary T cells from cord blood	blood
9	chr5:61581400-61587000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr5:61581600-61582800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr5:61581600-61582800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr5:61581800-61582800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr5:61581800-61582800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr5:61581800-61582800	Weak transcription	Esophagus	oesophagus
15	chr5:61581800-61587200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr5:61582200-61582600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr5:61582200-61582600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr5:61582200-61582600	Weak transcription	K562	blood
19	chr5:61582400-61583800	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr5:61582400-61584600	Enhancers	Primary T helper cells PMA-I stimulated	--

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