Variant report

Variant	rs12474598
Chromosome Location	chr2:32390368-32390369
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:62)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:62 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD2	chr2:32390238-32391251	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:32390270-32391813	MCF-7	breast:	n/a	n/a
3	MYBL2	chr2:32390279-32391538	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:32390279-32391296	GM12892	blood:	n/a	n/a
5	POLR2A	chr2:32390189-32391217	GM12891	blood:	n/a	n/a
6	CBX3	chr2:32390170-32391291	K562	blood:	n/a	n/a
7	POLR2A	chr2:32390242-32391647	PANC-1	pancreas:	n/a	n/a
8	MAX	chr2:32390361-32391172	K562	blood:	n/a	n/a
9	POLR2A	chr2:32390302-32391317	MCF-7	breast:	n/a	n/a
10	MYBL2	chr2:32389953-32391497	HepG2	liver:	n/a	n/a
11	POLR2A	chr2:32390221-32391903	GM12891	blood:	n/a	n/a
12	CHD2	chr2:32390197-32391584	K562	blood:	n/a	n/a
13	SIX5	chr2:32390253-32391708	A549	lung:	n/a	n/a
14	POLR2A	chr2:32390264-32391877	HepG2	liver:	n/a	n/a
15	GTF3C2	chr2:32389913-32391268	K562	blood:	n/a	n/a
16	POLR2A	chr2:32389104-32392168	K562	blood:	n/a	n/a
17	GABPA	chr2:32390251-32391925	MCF-7	breast:	n/a	n/a
18	SIN3AK20	chr2:32390357-32391435	HCT-116	colon:	n/a	n/a
19	POLR2A	chr2:32390193-32391372	GM12892	blood:	n/a	n/a
20	GTF3C2	chr2:32389942-32391096	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr2:32390227-32391323	GM12878	blood:	n/a	n/a
22	MAX	chr2:32390259-32391346	HCT-116	colon:	n/a	n/a
23	MAX	chr2:32390358-32391423	HepG2	liver:	n/a	n/a
24	POLR2A	chr2:32389843-32391924	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr2:32390359-32391894	K562	blood:	n/a	n/a
26	ZNF384	chr2:32390263-32391556	K562	blood:	n/a	n/a
27	HEY1	chr2:32390355-32391242	HepG2	liver:	n/a	chr2:32391190-32391205
28	POLR2A	chr2:32389652-32391597	PFSK-1	brain:	n/a	n/a
29	SP2	chr2:32390364-32391445	HepG2	liver:	n/a	n/a
30	UBTF	chr2:32390275-32392294	K562	blood:	n/a	n/a
31	POLR2A	chr2:32390126-32391596	SK-N-SH	brain:	n/a	n/a
32	MYC	chr2:32390010-32391167	MCF10A-Er-Src	breast:	n/a	chr2:32390094-32390105
33	SP1	chr2:32390341-32391377	HCT-116	colon:	n/a	chr2:32390896-32390910 chr2:32390895-32390906 chr2:32390896-32390905 chr2:32390895-32390907 chr2:32390896-32390906
34	CBX3	chr2:32390359-32391179	K562	blood:	n/a	n/a
35	REST	chr2:32390262-32391434	H1-neurons	neurons:	n/a	chr2:32390958-32390966 chr2:32391212-32391222 chr2:32390945-32390955
36	TAF1	chr2:32390226-32391614	A549	lung:	n/a	n/a
37	POLR2A	chr2:32390304-32391417	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr2:32390336-32391345	Hela-S3	cervix:	n/a	n/a
39	MXI1	chr2:32389629-32391587	IMR90	lung:	n/a	n/a
40	POLR2A	chr2:32390250-32391951	K562	blood:	n/a	n/a
41	GABPA	chr2:32390060-32391687	A549	lung:	n/a	n/a
42	POLR2A	chr2:32389831-32391818	MCF10A-Er-Src	breast:	n/a	n/a
43	MAX	chr2:32390346-32391363	K562	blood:	n/a	n/a
44	TCF12	chr2:32390268-32391552	A549	lung:	n/a	n/a
45	POU2F2	chr2:32390303-32391207	GM12878	blood:	n/a	n/a
46	POLR2A	chr2:32390257-32391484	GM12892	blood:	n/a	n/a
47	MXI1	chr2:32389527-32392277	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr2:32390350-32391283	U87	brain:	n/a	n/a
49	POLR2A	chr2:32390208-32391494	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr2:32390343-32391202	GM12891	blood:	n/a	n/a

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:32264450..32265171-chr2:32390311..32391216,2	MCF-7	breast:
2	chr2:32263820..32266854-chr2:32389080..32393861,5	MCF-7	breast:
3	chr14:23398094..23398622-chr2:32390241..32390980,2	Hela-S3	cervix:
4	chr2:32388440..32390986-chr2:32579691..32583834,6	K562	blood:
5	chr2:32287339..32289467-chr2:32389793..32392170,2	MCF-7	breast:
6	chr17:77751563..77752252-chr2:32390356..32391194,2	HCT-116	colon:
7	chr2:32390024..32393805-chr2:32579476..32583220,6	K562	blood:
8	chr2:32295719..32297694-chr2:32389118..32390763,2	K562	blood:
9	chr2:32263395..32265602-chr2:32389530..32391691,2	MCF-7	breast:
10	chr2:32264868..32267001-chr2:32389298..32391324,2	K562	blood:
11	chr2:32286352..32290626-chr2:32388602..32393371,12	K562	blood:
12	chr13:111365513..111366041-chr2:32390122..32390862,2	Hela-S3	cervix:
13	chr2:32389583..32392652-chr2:32503120..32506003,3	K562	blood:
14	chr2:32234641..32236375-chr2:32389314..32391737,5	MCF-7	breast:
15	chr2:32286363..32290764-chr2:32387862..32393371,13	K562	blood:
16	chr2:32287157..32290220-chr2:32389830..32392599,3	MCF-7	breast:
17	chr2:32233185..32238105-chr2:32388775..32395245,11	K562	blood:
18	chr2:32233077..32237611-chr2:32388376..32395245,10	K562	blood:
19	chr2:32388347..32391315-chr6:27100140..27102328,2	MCF-7	breast:
20	chr2:32390281..32391012-chr9:96213301..96214069,2	Hela-S3	cervix:
21	chr17:76355690..76356222-chr2:32390213..32391047,2	HCT-116	colon:
22	chr2:32389277..32392458-chr2:32500839..32506003,6	K562	blood:
23	chr2:32112402..32115115-chr2:32387877..32390821,4	K562	blood:
24	chr2:32264101..32266985-chr2:32387828..32391332,6	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NLRC4-3	chr2:32390115-32390826	ENSG00000272716.1

No data

Variant related genes	Relation type
SLC30A6	TF binding region
ENSG00000196787	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000162961	Chromatin interaction
ENSG00000153487	Chromatin interaction
ENSG00000184557	Chromatin interaction
ENSG00000115760	Chromatin interaction
ENSG00000021574	Chromatin interaction
ENSG00000048828	Chromatin interaction
ENSG00000173894	Chromatin interaction
ENSG00000100462	Chromatin interaction
ENSG00000119820	Chromatin interaction
ENSG00000162959	Chromatin interaction
ENSG00000134905	Chromatin interaction
ENSG00000188938	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10208246	0.91[ASN][1000 genomes]
rs11124278	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11676475	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11678119	0.87[ASN][1000 genomes]
rs11683760	0.80[ASN][1000 genomes]
rs11683842	0.80[ASN][1000 genomes]
rs11694630	0.87[ASN][1000 genomes]
rs12465351	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12995952	0.84[ASN][1000 genomes]
rs12997026	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13427170	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs212686	0.86[EUR][1000 genomes]
rs212687	0.86[EUR][1000 genomes]
rs212694	0.81[EUR][1000 genomes]
rs212703	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs212713	0.81[EUR][1000 genomes]
rs212738	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs212739	0.90[ASN][1000 genomes]
rs212740	0.81[EUR][1000 genomes]
rs212741	0.84[EUR][1000 genomes]
rs212743	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs212744	0.86[EUR][1000 genomes]
rs212748	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs212749	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs212753	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs212755	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs212757	0.85[EUR][1000 genomes]
rs212762	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2280973	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2366736	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2886393	0.82[ASN][1000 genomes]
rs34976640	0.82[ASN][1000 genomes]
rs3769602	0.88[ASN][1000 genomes]
rs4258846	0.87[ASN][1000 genomes]
rs4407291	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4519572	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4952209	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4952252	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56208031	0.82[AMR][1000 genomes]
rs6716179	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6717209	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6723154	0.80[ASN][1000 genomes]
rs7572964	0.84[ASN][1000 genomes]
rs7581432	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7588883	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7592239	0.85[ASN][1000 genomes]
rs7592356	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS 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 lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv833670	chr2:32295778-32481857	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh 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
3	nsv873778	chr2:32297984-32409007	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv817386	chr2:32332893-32724794	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1001038	chr2:32333378-32657112	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1009359	chr2:32333378-32725117	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv535613	chr2:32333378-32725117	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32389200-32392000	Active TSS	NHLF	lung
2	chr2:32389400-32390400	Flanking Active TSS	Dnd41	blood
3	chr2:32389400-32391600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:32389400-32391800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr2:32389400-32391800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:32389400-32392000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:32389400-32392600	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr2:32389400-32392600	Active TSS	K562	blood
9	chr2:32389600-32391600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:32389600-32391600	Active TSS	A549	lung
11	chr2:32389600-32391800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:32389600-32391800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:32389600-32391800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:32389600-32392200	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr2:32389600-32392200	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr2:32389600-32392200	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr2:32389800-32391200	Active TSS	Primary hematopoietic stem cells	blood
18	chr2:32389800-32391400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:32389800-32391400	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr2:32389800-32391400	Active TSS	Fetal Kidney	kidney
21	chr2:32389800-32391400	Active TSS	HMEC	breast
22	chr2:32389800-32391600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr2:32389800-32391600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:32389800-32391600	Active TSS	Aorta	Aorta
25	chr2:32389800-32391600	Active TSS	Brain Angular Gyrus	brain
26	chr2:32389800-32391600	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr2:32389800-32391600	Active TSS	Fetal Stomach	stomach
28	chr2:32389800-32391600	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr2:32389800-32391600	Active TSS	NH-A	brain
30	chr2:32389800-32391800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr2:32389800-32391800	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr2:32389800-32391800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:32389800-32391800	Active TSS	Stomach Mucosa	stomach
34	chr2:32389800-32392000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:32389800-32392000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:32389800-32392000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:32389800-32392200	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr2:32389800-32392200	Active TSS	H1 Cell Line	embryonic stem cell
39	chr2:32389800-32392200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:32389800-32392200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:32389800-32392200	Active TSS	Psoas Muscle	Psoas
42	chr2:32390000-32390400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
43	chr2:32390000-32390400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
44	chr2:32390000-32390400	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr2:32390000-32390400	Weak transcription	Spleen	Spleen
46	chr2:32390000-32391000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr2:32390000-32391000	Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr2:32390000-32391200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:32390000-32391200	Active TSS	Liver	Liver
50	chr2:32390000-32391200	Active TSS	Monocytes-CD14+_RO01746	blood

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