Variant report

Variant	rs28420399
Chromosome Location	chr2:12146992-12146993
allele	C/T
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	CHD2	chr2:12146958-12147585	H1-hESC	embryonic stem cell:	n/a	n/a
2	MYC	chr2:12146799-12147059	MCF10A-Er-Src	breast:	n/a	n/a
3	ATF2	chr2:12146969-12147467	H1-hESC	embryonic stem cell:	n/a	n/a
4	TEAD4	chr2:12146986-12147429	ECC-1	luminal epithelium:	n/a	chr2:12147182-12147191
5	TEAD4	chr2:12146911-12147459	H1-hESC	embryonic stem cell:	n/a	chr2:12147182-12147191
6	ATF2	chr2:12146952-12147399	H1-hESC	embryonic stem cell:	n/a	n/a
7	JUN	chr2:12146973-12147447	H1-hESC	embryonic stem cell:	n/a	chr2:12147192-12147205
8	JUND	chr2:12146990-12147337	H1-hESC	embryonic stem cell:	n/a	n/a
9	JUND	chr2:12146585-12147454	H1-hESC	embryonic stem cell:	n/a	n/a
10	KAP1	chr2:12146917-12147478	HEK293	kidney:	n/a	n/a
11	TEAD4	chr2:12146990-12147427	ECC-1	luminal epithelium:	n/a	chr2:12147182-12147191
12	MAFK	chr2:12146912-12147096	IMR90	lung:	n/a	n/a
13	ATF3	chr2:12146983-12147363	H1-hESC	embryonic stem cell:	n/a	chr2:12147196-12147207 chr2:12147194-12147207 chr2:12147196-12147204 chr2:12147193-12147208

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:12107920..12110681-chr2:12144590..12147172,2	K562	blood:

Variant related genes	Relation type
ENSG00000224184	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12463701	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12464227	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12469736	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12471363	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12472165	1.00[ASN][1000 genomes]
rs12475585	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12476249	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12478633	1.00[ASN][1000 genomes]
rs12478664	1.00[ASN][1000 genomes]
rs12478705	1.00[ASN][1000 genomes]
rs12991902	1.00[ASN][1000 genomes]
rs34506780	1.00[ASN][1000 genomes]
rs34819724	1.00[ASN][1000 genomes]
rs34900642	1.00[ASN][1000 genomes]
rs35954069	1.00[ASN][1000 genomes]
rs41378155	1.00[ASN][1000 genomes]
rs56260961	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58143595	1.00[ASN][1000 genomes]
rs59609793	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60195725	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60510807	1.00[ASN][1000 genomes]
rs60873627	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708806	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6715248	1.00[ASN][1000 genomes]
rs6715988	1.00[ASN][1000 genomes]
rs71446438	1.00[ASN][1000 genomes]
rs73915889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73915899	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73915902	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73918407	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73918410	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73918411	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73918413	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73918415	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73918416	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73918422	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73918423	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73918424	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73918425	1.00[AMR][1000 genomes]
rs73918426	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73918427	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73918432	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers 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	26 gene(s)	inside rSNPs	diseases
2	esv3433991	chr2:12146727-12147182	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:12137200-12148800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:12141400-12147200	Weak transcription	K562	blood
3	chr2:12144600-12147200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr2:12144800-12147000	Enhancers	Primary T cells from cord blood	blood
5	chr2:12145000-12147200	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr2:12145000-12147200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr2:12145000-12147400	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr2:12145000-12147400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:12145000-12147600	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr2:12145000-12149800	Enhancers	Primary B cells from peripheral blood	blood
11	chr2:12145200-12147000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr2:12145200-12147200	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr2:12145200-12147600	Enhancers	HUVEC	blood vessel
14	chr2:12145400-12147000	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr2:12145400-12147800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr2:12145600-12147000	Enhancers	Primary hematopoietic stem cells	blood
17	chr2:12145600-12147200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr2:12145600-12147400	Enhancers	Fetal Lung	lung
19	chr2:12145600-12147400	Enhancers	Fetal Muscle Leg	muscle
20	chr2:12145600-12147600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:12145600-12147600	Enhancers	NH-A	brain
22	chr2:12145600-12147800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:12145600-12147800	Enhancers	HSMM	muscle
24	chr2:12145800-12147400	Enhancers	Fetal Heart	heart
25	chr2:12145800-12147400	Enhancers	HMEC	breast
26	chr2:12145800-12147400	Enhancers	Osteobl	bone
27	chr2:12145800-12148000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:12145800-12148000	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr2:12146000-12147400	Enhancers	Fetal Stomach	stomach
30	chr2:12146000-12147600	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr2:12146000-12148000	Enhancers	Liver	Liver
32	chr2:12146200-12147200	Enhancers	NHEK	skin
33	chr2:12146200-12147400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:12146200-12147600	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr2:12146200-12147600	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr2:12146200-12147600	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr2:12146200-12147800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:12146400-12147200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr2:12146400-12147800	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr2:12146400-12148000	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr2:12146400-12148000	Weak transcription	NHLF	lung
42	chr2:12146400-12151000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:12146600-12147200	Enhancers	Fetal Kidney	kidney
44	chr2:12146600-12147400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:12146600-12147400	Weak transcription	Fetal Brain Female	brain
46	chr2:12146600-12147600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:12146600-12148000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:12146600-12148800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:12146600-12148800	Enhancers	GM12878-XiMat	blood
50	chr2:12146600-12148800	Weak transcription	HSMMtube	muscle

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