Variant report

Variant	rs2004864
Chromosome Location	chr12:122359045-122359046
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	GATA3	chr12:122358972-122359498	SK-N-SH	brain:	n/a	n/a
2	SPI1	chr12:122359008-122359342	HL-60	blood:	n/a	n/a
3	GATA3	chr12:122359006-122359398	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:122356337..122361793-chr12:122458841..122462522,5	MCF-7	breast:
2	chr12:122355691..122357856-chr12:122357924..122360707,2	MCF-7	breast:

Variant related genes	Relation type
WDR66	TF binding region
ENSG00000158023	Chromatin interaction
ENSG00000110987	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11043275	0.85[ASN][1000 genomes]
rs1824949	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2004863	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2076860	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3741581	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4522209	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55778445	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57298119	0.90[EUR][1000 genomes]
rs58025403	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58026220	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58158474	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58516770	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58642707	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59116149	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59178789	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59695002	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60620185	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6486792	0.90[EUR][1000 genomes]
rs6486793	0.90[EUR][1000 genomes]
rs7138299	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7138556	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7294535	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7294829	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7303779	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7314352	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7964151	0.90[EUR][1000 genomes]
rs830125	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs872781	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122354200-122363000	Weak transcription	Small Intestine	intestine
2	chr12:122355600-122364800	Weak transcription	K562	blood
3	chr12:122356000-122362600	Weak transcription	Hela-S3	cervix
4	chr12:122356200-122361600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:122356400-122361800	Weak transcription	HepG2	liver
6	chr12:122356400-122362600	Weak transcription	Ovary	ovary
7	chr12:122356400-122362600	Weak transcription	HMEC	breast
8	chr12:122356400-122363000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr12:122356600-122362600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:122356600-122362800	Weak transcription	HSMMtube	muscle
11	chr12:122356800-122361200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr12:122356800-122361600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:122356800-122361600	Weak transcription	A549	lung
14	chr12:122356800-122362600	Weak transcription	Fetal Heart	heart
15	chr12:122356800-122362800	Weak transcription	Left Ventricle	heart
16	chr12:122356800-122362800	Weak transcription	HSMM	muscle
17	chr12:122356800-122363000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr12:122357000-122359800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:122357000-122360200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr12:122357000-122360200	Weak transcription	Brain Germinal Matrix	brain
21	chr12:122357000-122360400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr12:122357000-122361400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr12:122357000-122361400	Weak transcription	GM12878-XiMat	blood
24	chr12:122357000-122361600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:122357000-122361600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:122357000-122361600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr12:122357000-122361600	Weak transcription	Adipose Nuclei	Adipose
28	chr12:122357000-122361600	Weak transcription	Fetal Muscle Leg	muscle
29	chr12:122357000-122361600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr12:122357000-122361800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:122357000-122361800	Weak transcription	Placenta	Placenta
32	chr12:122357000-122362000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr12:122357000-122362000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr12:122357000-122362000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr12:122357000-122362600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr12:122357000-122362600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:122357000-122362600	Weak transcription	Colon Smooth Muscle	Colon
38	chr12:122357000-122362600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr12:122357000-122362600	Weak transcription	Fetal Brain Male	brain
40	chr12:122357000-122362600	Weak transcription	Fetal Brain Female	brain
41	chr12:122357000-122362600	Weak transcription	Fetal Intestine Large	intestine
42	chr12:122357000-122362600	Weak transcription	Fetal Intestine Small	intestine
43	chr12:122357000-122362600	Weak transcription	Fetal Stomach	stomach
44	chr12:122357000-122362600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr12:122357000-122362600	Weak transcription	Right Ventricle	heart
46	chr12:122357000-122362600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr12:122357000-122362600	Weak transcription	Spleen	Spleen
48	chr12:122357000-122362600	Weak transcription	NH-A	brain
49	chr12:122357000-122362800	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr12:122357000-122362800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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