Variant report

Variant	rs13411468
Chromosome Location	chr2:64431261-64431262
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:97)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:97 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr2:64431075-64431964	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:64430653-64431717	GM12878	blood:	n/a	n/a
3	RELA	chr2:64430798-64432266	GM19099	blood:	n/a	n/a
4	SPI1	chr2:64431156-64431816	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:64430954-64431649	GM12892	blood:	n/a	n/a
6	POLR2A	chr2:64430727-64431801	GM12892	blood:	n/a	n/a
7	POLR2A	chr2:64430706-64432223	GM12878	blood:	n/a	n/a
8	TAF1	chr2:64431242-64431551	GM12878	blood:	n/a	n/a
9	WRNIP1	chr2:64431139-64431896	GM12878	blood:	n/a	n/a
10	SMC3	chr2:64431055-64431745	GM12878	blood:	n/a	n/a
11	EP300	chr2:64431055-64431815	GM12878	blood:	n/a	n/a
12	YY1	chr2:64431066-64431637	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:64431144-64431545	GM12891	blood:	n/a	n/a
14	POLR2A	chr2:64430912-64431756	GM12892	blood:	n/a	n/a
15	GATA3	chr2:64430803-64431376	MCF-7	breast:	n/a	n/a
16	SPI1	chr2:64431179-64431783	GM12891	blood:	n/a	n/a
17	CHD2	chr2:64431146-64431857	GM12878	blood:	n/a	n/a
18	EP300	chr2:64431141-64431694	GM12878	blood:	n/a	n/a
19	POLR2A	chr2:64431113-64431292	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr2:64431142-64431648	GM12878	blood:	n/a	n/a
21	POU2F2	chr2:64430982-64431784	GM12878	blood:	n/a	n/a
22	POLR2A	chr2:64431017-64431613	GM12891	blood:	n/a	n/a
23	EBF1	chr2:64431130-64431700	GM12878	blood:	n/a	n/a
24	TAF1	chr2:64431242-64431806	GM12878	blood:	n/a	n/a
25	MTA3	chr2:64430568-64432120	GM12878	blood:	n/a	n/a
26	POLR2A	chr2:64431099-64431493	GM12878	blood:	n/a	n/a
27	ZNF143	chr2:64431141-64431786	H1-hESC	embryonic stem cell:	n/a	n/a
28	FOXM1	chr2:64431063-64431893	GM12878	blood:	n/a	n/a
29	BCL3	chr2:64431231-64431798	GM12878	blood:	n/a	n/a
30	PML	chr2:64430679-64432345	GM12878	blood:	n/a	n/a
31	TAF1	chr2:64431235-64431577	GM12891	blood:	n/a	n/a
32	RFX5	chr2:64431107-64431794	GM12878	blood:	n/a	n/a
33	POLR2A	chr2:64431129-64431297	MCF-7	breast:	n/a	n/a
34	PAX5	chr2:64431194-64431766	GM12878	blood:	n/a	n/a
35	POU2F2	chr2:64431168-64431701	GM12891	blood:	n/a	n/a
36	POLR2A	chr2:64430718-64432098	GM12878	blood:	n/a	n/a
37	RCOR1	chr2:64430910-64431972	GM12878	blood:	n/a	n/a
38	NFIC	chr2:64430699-64432104	GM12878	blood:	n/a	n/a
39	MTA3	chr2:64430842-64432186	GM12878	blood:	n/a	n/a
40	RELA	chr2:64431094-64431977	GM18526	blood:	n/a	n/a
41	YY1	chr2:64431231-64431671	GM12892	blood:	n/a	n/a
42	STAT1	chr2:64430987-64431824	GM12878	blood:	n/a	n/a
43	RUNX3	chr2:64430970-64432075	GM12878	blood:	n/a	n/a
44	STAT5A	chr2:64431041-64431791	GM12878	blood:	n/a	n/a
45	HDAC2	chr2:64430978-64431323	MCF-7	breast:	n/a	n/a
46	POLR2A	chr2:64430758-64432288	GM12891	blood:	n/a	n/a
47	RELA	chr2:64431059-64431876	GM19193	blood:	n/a	n/a
48	POLR2A	chr2:64430915-64431736	GM12878	blood:	n/a	n/a
49	ZNF143	chr2:64431221-64431950	GM12878	blood:	n/a	n/a
50	ELF1	chr2:64431073-64432130	GM12878	blood:	n/a	chr2:64431637-64431650

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:64431245-64431295	NB4	blood:	n/a
2	chr2:64431245-64431295	HRCEpiC	kidney:	n/a
3	chr2:64431245-64431295	AG09319	gingival:	n/a
4	chr2:64431245-64431295	Caco-2	colon:	n/a
5	chr2:64431245-64431295	GM19239	blood:	n/a
6	chr2:64431245-64431295	ovcar-3	ovarian:	n/a
7	chr2:64431245-64431295	HCF	heart:	n/a
8	chr2:64431245-64431295	HPAEpiC	pulmonary alveolar:	n/a
9	chr2:64431245-64431295	IMR90	lung:	fetal
10	chr2:64431245-64431295	NT2-D1	testis:	n/a
11	chr2:64431245-64431295	HCPEpiC	choroid plexus:	n/a
12	chr2:64431245-64431295	HUVEC	blood vessel:	n/a
13	chr2:64431245-64431295	K562	blood:	n/a
14	chr2:64431245-64431295	HIPEpiC	eye:	n/a
15	chr2:64431245-64431295	NHDF-neo	bronchial:	n/a
16	chr2:64431245-64431295	HRPEpiC	eye:	n/a
17	chr2:64431245-64431295	HL-60	blood:	n/a
18	chr2:64431245-64431295	T-47D	breast:	n/a
19	chr2:64431245-64431295	HAEpiC	amniotic membrane:	n/a
20	chr2:64431245-64431295	HRE	kidney:	n/a
21	chr2:64431245-64431295	AG10803	skin:	n/a
22	chr2:64431245-64431295	BE2_C	brain:	n/a
23	chr2:64431245-64431295	GM12892	blood:	n/a
24	chr2:64431245-64431295	NHBE	bronchial:	n/a
25	chr2:64431245-64431295	Hepatocyte	liver:	n/a
26	chr2:64431245-64431295	AG04450	lung:	fetal
27	chr2:64431245-64431295	HEK293	kidney:	embryo
28	chr2:64431245-64431295	GM06990	blood:	n/a
29	chr2:64431245-64431295	PFSK-1	brain:	n/a
30	chr2:64431245-64431295	U87	brain:	n/a
31	chr2:64431245-64431295	NH-A	brain:	n/a
32	chr2:64431245-64431295	HMEC	breast:	n/a
33	chr2:64431245-64431295	Jurkat	blood:	n/a
34	chr2:64431245-64431295	HCT-116	colon:	n/a
35	chr2:64431245-64431295	GM12891	blood:	n/a
36	chr2:64431245-64431295	ProgFib	skin:	n/a
37	chr2:64431245-64431295	AG04449	skin:	fetal
38	chr2:64431245-64431295	A549	lung:	n/a
39	chr2:64431245-64431295	GM12878	blood:	n/a
40	chr2:64431245-64431295	AG09309	skin:	n/a
41	chr2:64431245-64431295	SK-N-SH	brain:	n/a
42	chr2:64431245-64431295	HepG2	liver:	n/a
43	chr2:64431245-64431295	PANC-1	pancreas:	n/a
44	chr2:64431245-64431295	SK-N-SH_RA	brain:	n/a
45	chr2:64431245-64431295	MCF10A-Er-Src	breast:	n/a
46	chr2:64431245-64431295	H1-hESC	embryonic stem cell:	embryo
47	chr2:64431245-64431295	RPTEC	kidney:	n/a
48	chr2:64431245-64431295	HNPCEpiC	eye:	n/a
49	chr2:64431245-64431295	SAEC	small airway:	n/a
50	chr2:64431245-64431295	MCF-7	breast:	n/a

No data

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PELI1-2	chr2:64430424-64432619	XLOC_002123
2	lnc-PELI1-2	chr2:64430424-64432619	NR_033837
3	lnc-PELI1-2	chr2:64430424-64432619	NONHSAT071093

No data

Variant related genes	Relation type
ENSG00000225889	TF binding region
ENSG00000225889	CpG island

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10179276	1.00[AMR][1000 genomes]
rs10181595	1.00[AMR][1000 genomes]
rs13384491	1.00[AMR][1000 genomes]
rs13386653	1.00[AMR][1000 genomes]
rs13391343	1.00[AMR][1000 genomes]
rs13394672	1.00[AMR][1000 genomes]
rs13402981	1.00[AMR][1000 genomes]
rs13403474	1.00[AMR][1000 genomes]
rs13415878	1.00[AMR][1000 genomes]
rs13416589	1.00[AMR][1000 genomes]
rs13423144	1.00[AMR][1000 genomes]
rs13425328	1.00[AMR][1000 genomes]
rs13425693	1.00[AMR][1000 genomes]
rs13426558	1.00[AMR][1000 genomes]
rs13427994	1.00[AMR][1000 genomes]
rs13428769	1.00[AMR][1000 genomes]
rs6742704	1.00[AMR][1000 genomes]
rs7579814	1.00[AMR][1000 genomes]
rs7587919	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757803	chr2:64253005-64539556	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv2759055	chr2:64253005-64539556	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer 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	27 gene(s)	inside rSNPs	diseases
5	nsv428396	chr2:64253005-64539556	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	esv34698	chr2:64312142-64521366	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	esv34955	chr2:64312182-64521290	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv834243	chr2:64316514-64476935	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1006553	chr2:64339907-64764771	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv9957	chr2:64341714-64518231	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	esv13275	chr2:64342247-64515169	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv1012905	chr2:64342469-64508983	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
13	nsv1013735	chr2:64342469-64512286	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
14	esv3693324	chr2:64342469-64513207	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
15	nsv999608	chr2:64342469-64517459	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
16	nsv1000390	chr2:64343861-64512286	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
17	esv2756924	chr2:64349202-64521290	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
18	nsv1004574	chr2:64360195-64478171	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
19	nsv1004899	chr2:64369300-64513607	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
20	nsv535769	chr2:64369300-64513607	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
21	nsv1015084	chr2:64369734-64512286	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
22	nsv874237	chr2:64402689-64479060	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64416800-64438000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:64424400-64440000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:64425200-64436400	Weak transcription	K562	blood
4	chr2:64429200-64432000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:64429200-64432000	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr2:64429200-64433000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:64429400-64431600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:64429400-64431800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:64429400-64432200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:64429800-64432800	Enhancers	Fetal Kidney	kidney
11	chr2:64430000-64431600	Weak transcription	Fetal Heart	heart
12	chr2:64430200-64432000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr2:64430200-64432200	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr2:64430400-64432000	Enhancers	NH-A	brain
15	chr2:64430400-64432200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr2:64430600-64431400	Enhancers	Small Intestine	intestine
17	chr2:64430600-64431600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:64430600-64431600	Enhancers	HSMMtube	muscle
19	chr2:64430600-64431800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:64430600-64431800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:64430600-64431800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
22	chr2:64430600-64432000	Flanking Active TSS	GM12878-XiMat	blood
23	chr2:64430600-64432000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr2:64430600-64432200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:64430600-64432200	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr2:64430600-64432200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr2:64430600-64432200	Enhancers	Placenta Amnion	Placenta Amnion
28	chr2:64430600-64432200	Enhancers	HMEC	breast
29	chr2:64430600-64432800	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr2:64430800-64431400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:64430800-64431400	Enhancers	Right Ventricle	heart
32	chr2:64430800-64431600	Enhancers	H1 Cell Line	embryonic stem cell
33	chr2:64430800-64431600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:64430800-64431600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:64430800-64431600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr2:64430800-64431600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:64430800-64431600	Enhancers	Esophagus	oesophagus
38	chr2:64430800-64431600	Flanking Active TSS	Stomach Mucosa	stomach
39	chr2:64430800-64431600	Flanking Active TSS	NHEK	skin
40	chr2:64430800-64431600	Flanking Active TSS	NHLF	lung
41	chr2:64430800-64431800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:64430800-64431800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
43	chr2:64430800-64431800	Flanking Active TSS	Primary T cells from cord blood	blood
44	chr2:64430800-64431800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr2:64430800-64431800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr2:64430800-64431800	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr2:64430800-64431800	Flanking Active TSS	Brain Cingulate Gyrus	brain
48	chr2:64430800-64431800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr2:64430800-64431800	Flanking Active TSS	Rectal Smooth Muscle	rectum
50	chr2:64430800-64431800	Flanking Active TSS	Stomach Smooth Muscle	stomach

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