Variant report

Variant	rs2029986
Chromosome Location	chr12:25102192-25102193
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	CEBPB	chr12:25101772-25102434	A549	lung:	n/a	chr12:25102073-25102084
2	POLR2A	chr12:25099831-25105595	GM12892	blood:	n/a	n/a
3	CEBPB	chr12:25101863-25102270	A549	lung:	n/a	chr12:25102073-25102084
4	POLR2A	chr12:25101649-25102433	K562	blood:	n/a	n/a
5	POLR2A	chr12:25099474-25105917	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:25101730-25102327	A549	lung:	n/a	n/a
7	POU2F2	chr12:25101867-25102234	GM12891	blood:	n/a	n/a
8	POLR2A	chr12:25101805-25102332	A549	lung:	n/a	n/a
9	RCOR1	chr12:25101730-25102574	K562	blood:	n/a	n/a
10	POLR2A	chr12:25101229-25102528	HL-60	blood:	n/a	n/a
11	MXI1	chr12:25101396-25102462	H1-hESC	embryonic stem cell:	n/a	chr12:25102392-25102407
12	FOXM1	chr12:25100597-25102467	GM12878	blood:	n/a	n/a
13	MYC	chr12:25099506-25102659	K562	blood:	n/a	chr12:25102076-25102085
14	REST	chr12:25101763-25102208	K562	blood:	n/a	chr12:25101978-25101998 chr12:25101964-25101977 chr12:25102100-25102113
15	CTCF	chr12:25101988-25102199	Gliobla	brain:	n/a	n/a
16	ATF3	chr12:25101943-25102227	HepG2	liver:	n/a	n/a
17	CTCF	chr12:25102060-25102210	GM06990	blood:	n/a	n/a
18	CTCF	chr12:25101877-25102288	GM12878	blood:	n/a	n/a
19	MAZ	chr12:25101876-25102242	HepG2	liver:	n/a	chr12:25102076-25102085
20	POLR2A	chr12:25101200-25102596	PFSK-1	brain:	n/a	n/a
21	ATF3	chr12:25101881-25102522	K562	blood:	n/a	chr12:25102308-25102318
22	BCL3	chr12:25101855-25102292	GM12878	blood:	n/a	chr12:25102101-25102114
23	MAZ	chr12:25101256-25102822	K562	blood:	n/a	chr12:25102076-25102085
24	STAT5A	chr12:25100663-25102513	GM12878	blood:	n/a	n/a
25	MYC	chr12:25099632-25102671	K562	blood:	n/a	chr12:25102076-25102085
26	MAX	chr12:25101247-25102706	SK-N-SH	brain:	n/a	chr12:25102076-25102085
27	ELK1	chr12:25101936-25102423	K562	blood:	n/a	n/a
28	SP1	chr12:25101312-25102504	A549	lung:	n/a	chr12:25101395-25101409
29	POLR2A	chr12:25100739-25102574	H1-hESC	embryonic stem cell:	n/a	n/a
30	CEBPB	chr12:25101942-25102225	K562	blood:	n/a	chr12:25102073-25102084
31	GTF2F1	chr12:25100795-25102339	H1-hESC	embryonic stem cell:	n/a	n/a
32	TEAD4	chr12:25101841-25102275	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr12:25101827-25102390	K562	blood:	n/a	n/a
34	CTCF	chr12:25101936-25102223	GM12892	blood:	n/a	n/a
35	POLR2A	chr12:25101270-25102502	GM15510	blood:	n/a	n/a
36	TAF7	chr12:25100768-25102398	H1-hESC	embryonic stem cell:	n/a	n/a
37	TAF1	chr12:25101883-25102202	GM12878	blood:	n/a	n/a
38	ZBTB7A	chr12:25101794-25102239	ECC-1	luminal epithelium:	n/a	n/a
39	E2F6	chr12:25101492-25102385	A549	lung:	n/a	n/a
40	PML	chr12:25101654-25102289	K562	blood:	n/a	n/a
41	POLR2A	chr12:25101442-25102343	U87	brain:	n/a	n/a
42	FOXP2	chr12:25101887-25102304	SK-N-MC	brain:	n/a	n/a
43	CEBPB	chr12:25101573-25102376	H1-hESC	embryonic stem cell:	n/a	chr12:25102073-25102084
44	MTA3	chr12:25100193-25106014	GM12878	blood:	n/a	n/a
45	HDAC2	chr12:25101887-25102225	HepG2	liver:	n/a	n/a
46	CTBP2	chr12:25101387-25102425	H1-hESC	embryonic stem cell:	n/a	n/a
47	FOS	chr12:25101927-25102508	HUVEC	blood vessel:	n/a	chr12:25102226-25102235
48	POLR2A	chr12:25101407-25102216	ProgFib	skin:	n/a	n/a
49	MYC	chr12:25101842-25102195	MCF-7	breast:	n/a	chr12:25102076-25102085
50	ZC3H11A	chr12:25101902-25102518	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:25101914..25102596-chr17:2414791..2415294,2	NB4	blood:
2	chr12:24856687..24858774-chr12:25101784..25103304,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRMP-2	chr12:25102097-25102264	ENSG00000255921.1

Variant related genes	Relation type
BCAT1	TF binding region
ENSG00000255745	Chromatin interaction
ENSG00000127804	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10505955	1.00[YRI][hapmap]
rs10771141	1.00[YRI][hapmap]
rs10842427	1.00[YRI][hapmap]
rs10842433	1.00[YRI][hapmap]
rs11047709	1.00[YRI][hapmap]
rs11608526	1.00[YRI][hapmap]
rs11610069	1.00[YRI][hapmap]
rs1391028	1.00[YRI][hapmap]
rs17323781	1.00[MEX][hapmap];0.83[TSI][hapmap]
rs17376782	1.00[MEX][hapmap];0.83[TSI][hapmap]
rs1813470	1.00[YRI][hapmap]
rs4031159	0.85[YRI][hapmap]
rs4963596	1.00[YRI][hapmap]
rs4963820	1.00[YRI][hapmap]
rs4963839	0.90[TSI][hapmap]
rs4963843	1.00[MEX][hapmap];0.83[TSI][hapmap]
rs7305924	1.00[YRI][hapmap]
rs7954529	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422312	chr12:24519392-25221686	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv898920	chr12:24648863-25147192	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers 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 miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv932477	chr12:24705151-25346677	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv1067577	chr12:24791283-25346677	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv529514	chr12:24791283-25346677	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1041221	chr12:24880443-25213168	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv541425	chr12:24880443-25213168	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv469170	chr12:24891175-25204353	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
11	nsv557776	chr12:24891175-25204353	Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv557777	chr12:24891175-25205241	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
13	nsv469173	chr12:24891175-25207653	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
14	nsv557778	chr12:24891175-25207653	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	nsv1049138	chr12:24921100-25164524	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
16	nsv1051319	chr12:24921100-25238936	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
17	nsv1051968	chr12:24941350-25138118	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
18	nsv541427	chr12:24941350-25138118	Active TSS Genic enhancers Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
19	nsv1037288	chr12:24941350-25238936	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
20	nsv541428	chr12:24941350-25238936	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
21	nsv1041218	chr12:24972019-25304356	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
22	nsv832353	chr12:25060820-25119975	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
23	esv3378403	chr12:25084023-25181017	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25098400-25102600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr12:25099000-25102200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr12:25099000-25102200	Active TSS	K562	blood
4	chr12:25099200-25102200	Active TSS	Ovary	ovary
5	chr12:25099200-25102400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr12:25099400-25102200	Active TSS	H1 Cell Line	embryonic stem cell
7	chr12:25099400-25102400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:25099400-25102600	Active TSS	H9 Cell Line	embryonic stem cell
9	chr12:25099400-25102800	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr12:25099400-25102800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:25099600-25102200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:25099600-25102400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:25099600-25102400	Active TSS	HSMMtube	muscle
14	chr12:25099600-25102600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr12:25099600-25102600	Active TSS	Pancreas	Pancrea
16	chr12:25099800-25102200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:25099800-25102200	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr12:25099800-25102400	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr12:25099800-25102400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:25099800-25102400	Active TSS	Placenta Amnion	Placenta Amnion
21	chr12:25099800-25102400	Active TSS	NHLF	lung
22	chr12:25099800-25102600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:25099800-25102800	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr12:25100000-25102400	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr12:25100000-25102400	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr12:25100000-25102600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr12:25100000-25102600	Active TSS	HSMM	muscle
28	chr12:25100200-25102200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:25100200-25102200	Active TSS	A549	lung
30	chr12:25100200-25102400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
31	chr12:25100200-25102400	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
32	chr12:25100400-25102200	Active TSS	NH-A	brain
33	chr12:25100600-25102200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:25100600-25102200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:25100600-25102200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:25100600-25102200	Active TSS	Fetal Lung	lung
37	chr12:25100600-25102200	Active TSS	Osteobl	bone
38	chr12:25100600-25102400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr12:25100600-25102400	Active TSS	Colon Smooth Muscle	Colon
40	chr12:25100600-25102400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
41	chr12:25100600-25102400	Active TSS	Thymus	Thymus
42	chr12:25100600-25102400	Active TSS	NHDF-Ad	bronchial
43	chr12:25100600-25102600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:25100800-25102200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
45	chr12:25100800-25102200	Active TSS	Rectal Smooth Muscle	rectum
46	chr12:25100800-25102400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:25101000-25102200	Active TSS	Muscle Satellite Cultured Cells	--
48	chr12:25101000-25102200	Active TSS	Aorta	Aorta
49	chr12:25101000-25102200	Active TSS	Brain Anterior Caudate	brain
50	chr12:25101000-25102400	Flanking Active TSS	Adipose Nuclei	Adipose

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