Variant report

Variant	rs6897129
Chromosome Location	chr5:61900110-61900111
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:61898028..61900560-chr5:61910431..61912053,2	MCF-7	breast:
2	chr5:61897835..61900758-chr5:61901696..61904448,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10051610	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10053650	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10065349	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10078786	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12516160	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12521329	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13167856	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13176954	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13185924	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs181912	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1862569	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs190444	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2112982	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs255390	0.81[EUR][1000 genomes]
rs26623	0.81[EUR][1000 genomes]
rs26624	0.81[EUR][1000 genomes]
rs26625	0.81[EUR][1000 genomes]
rs26645	0.81[EUR][1000 genomes]
rs32049	0.80[EUR][1000 genomes]
rs32050	0.80[EUR][1000 genomes]
rs32150	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs32154	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs32155	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs32158	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs32164	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs32166	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs32168	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs32171	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs32174	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs32181	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs32186	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs32187	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs32188	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs39923	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs39934	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs39935	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4700012	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4700498	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4700499	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4700501	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7706610	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7709562	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7718484	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7735107	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7735741	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[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	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
3	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
4	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
5	nsv1020713	chr5:61786309-61921150	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv537770	chr5:61786309-61921150	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv881731	chr5:61794164-61941043	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
8	nsv881732	chr5:61811970-62063366	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv881734	chr5:61828147-61921815	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	esv2763458	chr5:61852234-62157166	ZNF genes & repeats Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
11	nsv1022817	chr5:61853619-62149259	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
12	nsv948334	chr5:61891622-62197219	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6897129	KIF2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61793600-61905000	Weak transcription	NHEK	skin
2	chr5:61803000-61904400	Weak transcription	Fetal Kidney	kidney
3	chr5:61848200-61939600	Weak transcription	Brain Anterior Caudate	brain
4	chr5:61856400-61906400	Weak transcription	Colon Smooth Muscle	Colon
5	chr5:61861400-61902600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr5:61862200-61902600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr5:61863200-61910200	Weak transcription	Right Ventricle	heart
8	chr5:61864800-61945800	Weak transcription	HSMMtube	muscle
9	chr5:61875000-61906600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr5:61875000-61922200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr5:61876200-61904400	Weak transcription	Fetal Muscle Leg	muscle
12	chr5:61879600-61908800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:61881400-61939400	Weak transcription	Spleen	Spleen
14	chr5:61881800-61901200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr5:61881800-61905200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:61882000-61916400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr5:61882200-61902600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr5:61882200-61925400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr5:61883400-61925800	Weak transcription	Psoas Muscle	Psoas
20	chr5:61884000-61910200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr5:61885800-61904400	Weak transcription	Brain Hippocampus Middle	brain
22	chr5:61886800-61941200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr5:61887000-61912000	Weak transcription	Brain Angular Gyrus	brain
24	chr5:61887000-61922800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr5:61887400-61903800	Weak transcription	Placenta	Placenta
26	chr5:61888600-61901000	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr5:61888800-61901600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr5:61888800-61904800	Weak transcription	Fetal Intestine Small	intestine
29	chr5:61888800-61905000	Weak transcription	GM12878-XiMat	blood
30	chr5:61888800-61905600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr5:61888800-61910400	Weak transcription	Lung	lung
32	chr5:61888800-61928000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr5:61888800-61937000	Weak transcription	Gastric	stomach
34	chr5:61889000-61901200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr5:61889000-61905200	Weak transcription	Fetal Thymus	thymus
36	chr5:61889200-61904400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr5:61889200-61923400	Weak transcription	A549	lung
38	chr5:61889400-61907200	Weak transcription	HMEC	breast
39	chr5:61889400-61907600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr5:61889600-61901200	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr5:61889600-61925400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr5:61889600-61929200	Weak transcription	NH-A	brain
43	chr5:61889600-61936200	Weak transcription	Primary B cells from peripheral blood	blood
44	chr5:61890600-61902600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr5:61890800-61905000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr5:61891000-61902600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr5:61891000-61905800	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr5:61891000-61909400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr5:61891000-61910200	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr5:61891000-61910200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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