Variant report

Variant	rs3776612
Chromosome Location	chr5:61603423-61603424
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	ZNF384	chr5:61602991-61603499	GM12878	blood:	n/a	n/a
2	EP300	chr5:61602868-61603432	GM12878	blood:	n/a	chr5:61603196-61603210
3	CHD2	chr5:61603256-61603452	K562	blood:	n/a	n/a
4	HCFC1	chr5:61600977-61603460	Hela-S3	cervix:	n/a	n/a
5	NFATC1	chr5:61602782-61603463	GM12878	blood:	n/a	n/a
6	SIN3A	chr5:61602887-61603674	GM12878	blood:	n/a	n/a
7	BCLAF1	chr5:61602781-61603443	GM12878	blood:	n/a	n/a
8	MXI1	chr5:61600891-61603632	SK-N-SH	brain:	n/a	chr5:61601697-61601706 chr5:61601697-61601706 chr5:61601695-61601704
9	E2F6	chr5:61602232-61603523	H1-hESC	embryonic stem cell:	n/a	chr5:61602800-61602812 chr5:61602798-61602807
10	CHD1	chr5:61602328-61603430	GM12878	blood:	n/a	n/a
11	REST	chr5:61601132-61603545	H1-neurons	neurons:	n/a	chr5:61601916-61601929 chr5:61603039-61603048 chr5:61602540-61602550
12	MAZ	chr5:61601149-61603480	IMR90	lung:	n/a	chr5:61601694-61601707 chr5:61601696-61601706 chr5:61601695-61601704 chr5:61601695-61601705 chr5:61602701-61602711 chr5:61601694-61601707 chr5:61601695-61601706 chr5:61601696-61601706 chr5:61601695-61601705 chr5:61601694-61601707 chr5:61601696-61601705 chr5:61601696-61601705 chr5:61601913-61601923 chr5:61601694-61601707 chr5:61601696-61601705 chr5:61601695-61601706 chr5:61601695-61601706
13	MYC	chr5:61601077-61603440	K562	blood:	n/a	chr5:61601694-61601707 chr5:61601696-61601706 chr5:61601695-61601704 chr5:61601695-61601705 chr5:61602701-61602711 chr5:61601694-61601704 chr5:61601694-61601707 chr5:61601695-61601706 chr5:61601696-61601706 chr5:61601695-61601705 chr5:61601694-61601707 chr5:61601696-61601705 chr5:61601696-61601705 chr5:61601913-61601923 chr5:61601694-61601707 chr5:61601696-61601705 chr5:61601695-61601706 chr5:61601695-61601706
14	MXI1	chr5:61601305-61603454	GM12878	blood:	n/a	chr5:61601697-61601706 chr5:61601697-61601706 chr5:61601695-61601704
15	MTA3	chr5:61601125-61603429	GM12878	blood:	n/a	n/a
16	MAX	chr5:61600960-61603925	K562	blood:	n/a	chr5:61601694-61601707 chr5:61601696-61601706 chr5:61601695-61601704 chr5:61601695-61601705 chr5:61602701-61602711 chr5:61601694-61601704 chr5:61601694-61601707 chr5:61601695-61601706 chr5:61601696-61601706 chr5:61601695-61601705 chr5:61603817-61603827 chr5:61603816-61603827 chr5:61601694-61601707 chr5:61601696-61601705 chr5:61601696-61601705 chr5:61603818-61603825 chr5:61601913-61601923 chr5:61601694-61601707 chr5:61601696-61601705 chr5:61601695-61601706 chr5:61601695-61601706
17	E2F6	chr5:61602776-61603469	A549	lung:	n/a	chr5:61602800-61602812 chr5:61602798-61602807
18	SIN3A	chr5:61601400-61603427	H1-hESC	embryonic stem cell:	n/a	chr5:61601697-61601706 chr5:61602140-61602148 chr5:61602541-61602550
19	ZMIZ1	chr5:61603411-61603468	K562	blood:	n/a	n/a
20	MXI1	chr5:61601340-61603521	IMR90	lung:	n/a	chr5:61601697-61601706 chr5:61601697-61601706 chr5:61601695-61601704
21	WRNIP1	chr5:61602873-61603877	GM12878	blood:	n/a	n/a
22	POLR2A	chr5:61602732-61603542	GM12878	blood:	n/a	n/a
23	ZNF384	chr5:61602869-61603605	K562	blood:	n/a	n/a
24	MAX	chr5:61601185-61603493	A549	lung:	n/a	chr5:61601694-61601707 chr5:61601696-61601706 chr5:61601695-61601704 chr5:61601695-61601705 chr5:61602701-61602711 chr5:61601694-61601704 chr5:61601694-61601707 chr5:61601695-61601706 chr5:61601696-61601706 chr5:61601695-61601705 chr5:61601694-61601707 chr5:61601696-61601705 chr5:61601696-61601705 chr5:61601913-61601923 chr5:61601694-61601707 chr5:61601696-61601705 chr5:61601695-61601706 chr5:61601695-61601706
25	MYC	chr5:61602874-61603432	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:61602672..61603442-chr7:75544017..75544556,2	Hela-S3	cervix:
2	chr5:61601799..61604714-chr5:61698844..61701505,2	MCF-7	breast:
3	chr5:61591991..61594374-chr5:61603392..61605599,2	K562	blood:
4	chr5:61601958..61603491-chr5:61698096..61700949,2	MCF-7	breast:
5	chr5:61601533..61603969-chr5:61707379..61709702,2	K562	blood:

Variant related genes	Relation type
KIF2A	TF binding region
ENSG00000265020	Chromatin interaction
ENSG00000127948	Chromatin interaction
ENSG00000086189	Chromatin interaction
ENSG00000086200	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1108158	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11740652	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11742167	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11747516	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12655562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13155253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13156073	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13156695	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13161789	0.87[AMR][1000 genomes]
rs13162519	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13163533	0.86[EUR][1000 genomes]
rs13169321	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13170425	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13174779	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13176923	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13178729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13181377	0.87[AMR][1000 genomes]
rs13189446	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13190153	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs153864	0.84[ASN][1000 genomes]
rs16875037	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890613	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16890618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890628	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890634	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2059162	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2063255	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2272291	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs246198	0.82[ASN][1000 genomes]
rs27090	0.80[ASN][1000 genomes]
rs34220654	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34596001	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35238667	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35311093	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35572300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35672643	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35699711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35744020	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35746052	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35794032	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35808056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35815430	0.96[EUR][1000 genomes]
rs35842742	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36105063	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3776614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822487	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4289514	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71617425	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71617426	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71617427	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71617428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71617429	0.88[EUR][1000 genomes]
rs7446543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs971965	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
10	esv3355830	chr5:61601020-61603768	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3776612	KIF2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61601200-61603800	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr5:61601200-61603800	Active TSS	Brain Hippocampus Middle	brain
3	chr5:61601200-61603800	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr5:61601200-61603800	Active TSS	Fetal Kidney	kidney
5	chr5:61601200-61603800	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr5:61601200-61604400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr5:61601400-61603600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:61601400-61603600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr5:61601400-61603600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:61601400-61603600	Active TSS	Ovary	ovary
11	chr5:61601400-61603800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:61601400-61604000	Active TSS	H9 Cell Line	embryonic stem cell
13	chr5:61601400-61604000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:61601600-61603600	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr5:61601600-61603600	Active TSS	Brain Angular Gyrus	brain
16	chr5:61601600-61603600	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr5:61601600-61603600	Active TSS	Fetal Lung	lung
18	chr5:61601600-61603800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr5:61601600-61603800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr5:61601600-61603800	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr5:61601600-61603800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:61601600-61603800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr5:61601600-61603800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:61601600-61603800	Active TSS	Brain Anterior Caudate	brain
25	chr5:61601600-61603800	Active TSS	Brain Substantia Nigra	brain
26	chr5:61601600-61603800	Active TSS	Colon Smooth Muscle	Colon
27	chr5:61601600-61603800	Active TSS	Rectal Mucosa Donor 31	rectum
28	chr5:61601600-61603800	Active TSS	Rectal Smooth Muscle	rectum
29	chr5:61601600-61603800	Active TSS	HSMM	muscle
30	chr5:61601600-61603800	Active TSS	NHDF-Ad	bronchial
31	chr5:61601600-61604000	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr5:61601600-61604000	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr5:61601600-61604000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr5:61601600-61604200	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr5:61601600-61604200	Active TSS	Right Atrium	heart
36	chr5:61601600-61604200	Active TSS	HSMMtube	muscle
37	chr5:61601600-61604400	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr5:61601800-61603600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr5:61601800-61603600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:61601800-61603600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr5:61601800-61603600	Active TSS	Muscle Satellite Cultured Cells	--
42	chr5:61601800-61603600	Active TSS	Fetal Intestine Large	intestine
43	chr5:61601800-61603600	Active TSS	NHEK	skin
44	chr5:61601800-61603800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr5:61601800-61603800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:61601800-61603800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr5:61601800-61603800	Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr5:61601800-61603800	Active TSS	Colonic Mucosa	Colon
49	chr5:61601800-61603800	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr5:61601800-61603800	Active TSS	GM12878-XiMat	blood

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