Variant report

Variant	rs10044843
Chromosome Location	chr5:61606371-61606372
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr5:61606353-61606378	K562	blood:	n/a	n/a
2	CEBPD	chr5:61606239-61606770	K562	blood:	n/a	n/a
3	NR2F2	chr5:61606272-61606725	K562	blood:	n/a	n/a
4	TEAD4	chr5:61606169-61606790	K562	blood:	n/a	n/a
5	TBL1XR1	chr5:61606368-61606889	K562	blood:	n/a	n/a
6	TRIM28	chr5:61606286-61606779	K562	blood:	n/a	n/a
7	GATA2	chr5:61606232-61606652	K562	blood:	n/a	n/a
8	RCOR1	chr5:61606347-61606716	K562	blood:	n/a	n/a
9	WRNIP1	chr5:61606246-61606622	GM12878	blood:	n/a	n/a
10	CCNT2	chr5:61606227-61606721	K562	blood:	n/a	n/a
11	RCOR1	chr5:61606307-61606724	K562	blood:	n/a	n/a
12	PML	chr5:61606240-61606690	K562	blood:	n/a	n/a
13	STAT5A	chr5:61606254-61606750	K562	blood:	n/a	chr5:61606351-61606362 chr5:61606258-61606266
14	UBTF	chr5:61606347-61606547	K562	blood:	n/a	n/a
15	POLR2A	chr5:61606334-61606604	K562	blood:	n/a	n/a
16	GATA1	chr5:61606217-61606914	K562	blood:	n/a	n/a
17	ZC3H11A	chr5:61606355-61606571	K562	blood:	n/a	n/a
18	TEAD4	chr5:61606200-61606787	K562	blood:	n/a	n/a
19	GATA1	chr5:61606207-61607239	PBDE	blood:	n/a	chr5:61607068-61607079
20	TBL1XR1	chr5:61606370-61606780	K562	blood:	n/a	n/a
21	SPI1	chr5:61606261-61606453	GM12878	blood:	n/a	chr5:61606351-61606360
22	ZMIZ1	chr5:61606370-61606720	K562	blood:	n/a	n/a
23	CUX1	chr5:61606347-61606992	K562	blood:	n/a	n/a
24	ARID3A	chr5:61606306-61606906	K562	blood:	n/a	chr5:61606316-61606332 chr5:61606317-61606333
25	POLR2A	chr5:61606220-61606706	K562	blood:	n/a	n/a
26	POLR2A	chr5:61606259-61606856	K562	blood:	n/a	n/a
27	MYC	chr5:61606265-61606742	K562	blood:	n/a	n/a
28	GATA2	chr5:61606360-61606611	K562	blood:	n/a	n/a
29	CEBPD	chr5:61606200-61606837	K562	blood:	n/a	n/a
30	PML	chr5:61606304-61606769	K562	blood:	n/a	n/a
31	TAL1	chr5:61606321-61606734	K562	blood:	n/a	n/a
32	JUND	chr5:61606313-61606780	K562	blood:	n/a	chr5:61606617-61606626
33	EP300	chr5:61606320-61606849	K562	blood:	n/a	n/a
34	NR2F2	chr5:61606198-61606709	K562	blood:	n/a	n/a
35	ZNF384	chr5:61606353-61606817	K562	blood:	n/a	n/a
36	IRF1	chr5:61606290-61606981	K562	blood:	n/a	chr5:61606351-61606361 chr5:61606351-61606365 chr5:61606624-61606634 chr5:61606349-61606363 chr5:61606351-61606362 chr5:61606347-61606361

No.	Distal block	Cell Line	Cell type
1	chr5:61604944..61606842-chr5:61609048..61611891,3	MCF-7	breast:
2	chr5:61604639..61607587-chr5:61647579..61650088,2	MCF-7	breast:
3	chr5:61606018..61607564-chr5:61612889..61615038,2	MCF-7	breast:
4	chr5:61602098..61603608-chr5:61605633..61607272,2	MCF-7	breast:
5	chr5:61592874..61595599-chr5:61604099..61606788,3	K562	blood:

Variant related genes	Relation type
KIF2A	TF binding region
ENSG00000068796	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10471545	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13159750	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs152187	0.81[EUR][1000 genomes]
rs152188	0.81[EUR][1000 genomes]
rs152206	0.80[EUR][1000 genomes]
rs153862	0.81[EUR][1000 genomes]
rs2034240	0.83[AFR][1000 genomes]
rs2112884	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2344396	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs264530	0.83[AFR][1000 genomes]
rs26649	0.86[EUR][1000 genomes]
rs27542	0.86[EUR][1000 genomes]
rs35056	0.86[EUR][1000 genomes]
rs35057	0.83[EUR][1000 genomes]
rs35059	0.82[EUR][1000 genomes]
rs3846466	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs40108	0.82[EUR][1000 genomes]
rs4037273	0.81[AMR][1000 genomes]
rs4290970	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4700004	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56836756	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9291756	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[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
rs10044843	KIF2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61603200-61629200	Weak transcription	Lung	lung
2	chr5:61603200-61629200	Weak transcription	Spleen	Spleen
3	chr5:61603400-61606800	Weak transcription	Small Intestine	intestine
4	chr5:61603400-61607400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:61603400-61625200	Weak transcription	Stomach Mucosa	stomach
6	chr5:61603400-61658600	Weak transcription	Aorta	Aorta
7	chr5:61603600-61622200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:61603600-61622400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:61603600-61629200	Weak transcription	Psoas Muscle	Psoas
10	chr5:61603800-61606400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:61603800-61607600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr5:61603800-61607800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr5:61603800-61609600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:61603800-61611200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:61603800-61611200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr5:61603800-61611200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr5:61603800-61629200	Weak transcription	Left Ventricle	heart
18	chr5:61604000-61606400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr5:61604000-61606400	Weak transcription	Fetal Lung	lung
20	chr5:61604000-61606400	Weak transcription	Osteobl	bone
21	chr5:61604000-61606800	Weak transcription	Adipose Nuclei	Adipose
22	chr5:61604000-61607400	Weak transcription	Fetal Intestine Small	intestine
23	chr5:61604000-61607400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr5:61604000-61607800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:61604000-61607800	Weak transcription	Colon Smooth Muscle	Colon
26	chr5:61604000-61608000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr5:61604000-61611000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr5:61604000-61617400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr5:61604000-61622200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr5:61604000-61622200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr5:61604000-61622200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr5:61604000-61629000	Weak transcription	Thymus	Thymus
33	chr5:61604200-61607000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr5:61604200-61609000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:61604200-61609000	Enhancers	Brain Anterior Caudate	brain
36	chr5:61604200-61609200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:61604200-61616800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr5:61604400-61606400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr5:61604400-61606400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:61604400-61606400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr5:61604400-61606400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr5:61604400-61606400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr5:61604400-61606400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr5:61604400-61606400	Weak transcription	Fetal Intestine Large	intestine
45	chr5:61604400-61606400	Weak transcription	HSMMtube	muscle
46	chr5:61604400-61606600	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr5:61604400-61607000	Weak transcription	HMEC	breast
48	chr5:61604400-61608200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr5:61604400-61608800	Enhancers	NHDF-Ad	bronchial
50	chr5:61604400-61616000	Enhancers	Primary T helper cells PMA-I stimulated	--

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