Variant report

Variant	rs153870
Chromosome Location	chr5:61755438-61755439
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:61747217..61749290-chr5:61754763..61757506,2	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs152187	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs152188	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs152206	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs153856	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs153857	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs153858	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs153861	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs153862	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs173522	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs181912	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs190444	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs247228	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs247229	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs247233	0.94[AFR][1000 genomes]
rs247234	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs247245	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs247247	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs255220	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs255390	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs26623	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs26624	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs26625	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs26628	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs26629	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs26630	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs26638	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs26645	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs26649	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs27447	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs27542	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs32048	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs32049	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs32050	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs32051	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs32150	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs32154	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs32155	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs32158	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs32164	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs32166	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs32168	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs32171	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs32174	0.84[ASN][1000 genomes]
rs32181	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs32186	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs32187	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs32188	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35010	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35013	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35056	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35057	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35059	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35060	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs39923	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs39934	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs39935	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs40108	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs706650	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
6	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
7	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
8	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
9	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
10	nsv881729	chr5:61719506-61857577	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv881730	chr5:61750667-61883581	Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs153870	KIF2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61709200-61770800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:61709400-61763400	Weak transcription	Aorta	Aorta
3	chr5:61709800-61769000	Weak transcription	NH-A	brain
4	chr5:61709800-61809200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr5:61722800-61770600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:61728400-61763400	Weak transcription	Pancreas	Pancrea
7	chr5:61728400-61807600	Weak transcription	Psoas Muscle	Psoas
8	chr5:61728800-61763000	Weak transcription	Fetal Brain Female	brain
9	chr5:61728800-61838200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr5:61730000-61834200	Weak transcription	Gastric	stomach
11	chr5:61731800-61764000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr5:61732800-61805200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:61733200-61756800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr5:61733600-61763000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr5:61738800-61763000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr5:61739200-61763000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr5:61739200-61763400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr5:61739200-61862800	Weak transcription	Brain Substantia Nigra	brain
19	chr5:61739600-61787800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr5:61743000-61763400	Weak transcription	Brain Angular Gyrus	brain
21	chr5:61744600-61764000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr5:61744800-61838600	Weak transcription	Colonic Mucosa	Colon
23	chr5:61746200-61783600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr5:61747800-61756400	Weak transcription	GM12878-XiMat	blood
25	chr5:61747800-61756800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:61748000-61794600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:61748000-61862800	Weak transcription	Right Ventricle	heart
28	chr5:61748400-61756600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr5:61748400-61761400	Weak transcription	HUVEC	blood vessel
30	chr5:61748400-61761600	Weak transcription	HSMM	muscle
31	chr5:61748400-61763200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr5:61748400-61763400	Weak transcription	Fetal Kidney	kidney
33	chr5:61748600-61763000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr5:61748600-61763000	Weak transcription	Placenta	Placenta
35	chr5:61748600-61763200	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr5:61748600-61763400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr5:61748600-61784400	Weak transcription	Lung	lung
38	chr5:61748600-61787000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr5:61748800-61756600	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr5:61748800-61761600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:61748800-61763400	Weak transcription	Spleen	Spleen
42	chr5:61748800-61763400	Weak transcription	HepG2	liver
43	chr5:61748800-61771400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr5:61749000-61756600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr5:61749000-61756600	Weak transcription	Fetal Lung	lung
46	chr5:61749000-61786200	Weak transcription	Brain Anterior Caudate	brain
47	chr5:61749200-61763400	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr5:61749200-61763400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr5:61749400-61763000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr5:61749400-61763000	Weak transcription	Brain Hippocampus Middle	brain

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