Variant report

Variant	rs873358
Chromosome Location	chr2:11888819-11888820
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	POLR2A	chr2:11886620-11891581	GM12878	blood:	n/a	n/a
2	EP300	chr2:11888640-11888840	GM12878	blood:	n/a	n/a
3	EP300	chr2:11888661-11891529	GM12878	blood:	n/a	chr2:11889573-11889587 chr2:11889511-11889527 chr2:11889056-11889070 chr2:11889113-11889122
4	WRNIP1	chr2:11887983-11890899	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:11886595-11892488	MCF10A-Er-Src	breast:	n/a	n/a
6	EBF1	chr2:11888626-11888962	GM12878	blood:	n/a	n/a
7	ELK1	chr2:11888689-11888981	GM12878	blood:	n/a	n/a
8	CHD1	chr2:11886735-11891594	GM12878	blood:	n/a	n/a
9	ZNF143	chr2:11888454-11889100	GM12878	blood:	n/a	chr2:11888789-11888807
10	CHD2	chr2:11888090-11891444	GM12878	blood:	n/a	n/a
11	RUNX3	chr2:11888578-11888913	GM12878	blood:	n/a	n/a
12	RCOR1	chr2:11888262-11891527	GM12878	blood:	n/a	n/a
13	MAZ	chr2:11888474-11891368	GM12878	blood:	n/a	chr2:11890696-11890706 chr2:11890692-11890707 chr2:11890695-11890706 chr2:11890695-11890705 chr2:11890697-11890706 chr2:11890694-11890709 chr2:11890694-11890707 chr2:11890696-11890705 chr2:11890694-11890707 chr2:11890695-11890706 chr2:11888946-11888956 chr2:11890694-11890707 chr2:11890696-11890705 chr2:11888796-11888806 chr2:11890695-11890706 chr2:11890697-11890704
14	MYC	chr2:11888229-11888990	K562	blood:	n/a	chr2:11888946-11888956 chr2:11888796-11888806
15	POLR2A	chr2:11888404-11891507	GM18505	blood:	n/a	n/a
16	SIN3A	chr2:11888726-11889313	GM12878	blood:	n/a	n/a
17	POLR2A	chr2:11886585-11888855	K562	blood:	n/a	n/a
18	MXI1	chr2:11886527-11889380	GM12878	blood:	n/a	n/a
19	ELF1	chr2:11888621-11889212	GM12878	blood:	n/a	chr2:11888753-11888765
20	POLR2A	chr2:11887260-11891538	GM12891	blood:	n/a	n/a
21	POLR2A	chr2:11888165-11891554	GM12878	blood:	n/a	n/a
22	POLR2A	chr2:11886566-11891563	GM12878	blood:	n/a	n/a
23	CTCF	chr2:11888760-11888910	GM12865	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:11886833..11889158-chr2:11909295..11910808,2	K562	blood:
2	chr2:11881178..11885762-chr2:11886043..11889477,7	MCF-7	breast:
3	chr2:11887777..11889810-chr2:11903193..11905347,2	K562	blood:
4	chr2:11882508..11884186-chr2:11887506..11889026,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230790	TF binding region
ENSG00000230790	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1006538	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs10169802	0.99[ASN][1000 genomes]
rs10185333	0.88[AFR][1000 genomes]
rs10192566	0.99[ASN][1000 genomes]
rs10205312	0.89[ASN][1000 genomes]
rs10205400	0.88[ASN][1000 genomes]
rs10207506	1.00[ASN][1000 genomes]
rs10208679	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10209969	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11676086	1.00[ASN][1000 genomes]
rs11693809	0.99[ASN][1000 genomes]
rs11897144	0.90[ASN][1000 genomes]
rs13407101	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13409154	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13412852	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1469952	0.84[ASN][1000 genomes]
rs2278513	0.84[ASN][1000 genomes]
rs2358041	0.90[ASN][1000 genomes]
rs2358042	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4076055	0.99[ASN][1000 genomes]
rs4315495	1.00[ASN][1000 genomes]
rs4669778	0.83[ASN][1000 genomes]
rs62113306	0.96[ASN][1000 genomes]
rs6717910	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6731096	0.96[ASN][1000 genomes]
rs72773975	0.88[AFR][1000 genomes]
rs72773994	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7595221	0.93[ASN][1000 genomes]
rs893342	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS 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 miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	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
4	nsv580973	chr2:11864946-11898931	Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv580974	chr2:11867841-11898931	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11887000-11890400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr2:11887000-11891600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:11887200-11889200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
4	chr2:11887200-11889200	Flanking Active TSS	Duodenum Mucosa	Duodenum
5	chr2:11887200-11889400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr2:11887200-11890400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
7	chr2:11887400-11889000	Flanking Active TSS	HUVEC	blood vessel
8	chr2:11887400-11889200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr2:11887400-11889200	Flanking Active TSS	K562	blood
10	chr2:11887400-11889600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:11887400-11889600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
12	chr2:11887400-11890400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:11887400-11890400	Enhancers	Spleen	Spleen
14	chr2:11887400-11890600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr2:11887600-11889000	Enhancers	H1 Cell Line	embryonic stem cell
16	chr2:11887600-11889000	Enhancers	Pancreas	Pancrea
17	chr2:11887600-11890400	Enhancers	Fetal Muscle Trunk	muscle
18	chr2:11887600-11890600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:11887600-11891200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr2:11887600-11891400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:11887800-11889000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:11887800-11889000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr2:11887800-11889000	Enhancers	Small Intestine	intestine
24	chr2:11887800-11889000	Flanking Active TSS	HMEC	breast
25	chr2:11887800-11889600	Flanking Active TSS	HepG2	liver
26	chr2:11887800-11889800	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr2:11887800-11889800	Flanking Active TSS	NHEK	skin
28	chr2:11887800-11890000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:11887800-11891400	Enhancers	Fetal Muscle Leg	muscle
30	chr2:11887800-11894000	Enhancers	Primary B cells from peripheral blood	blood
31	chr2:11888000-11889000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:11888000-11889400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:11888000-11889400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:11888000-11889400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:11888000-11889600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:11888000-11889600	Flanking Active TSS	Right Ventricle	heart
37	chr2:11888000-11890000	Weak transcription	HSMMtube	muscle
38	chr2:11888000-11890400	Enhancers	Fetal Brain Male	brain
39	chr2:11888000-11891400	Enhancers	Primary B cells from cord blood	blood
40	chr2:11888000-11891600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr2:11888000-11891600	Flanking Active TSS	GM12878-XiMat	blood
42	chr2:11888000-11891800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:11888200-11889000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr2:11888200-11889000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
45	chr2:11888200-11889200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
46	chr2:11888200-11889200	Enhancers	Colon Smooth Muscle	Colon
47	chr2:11888200-11889200	Flanking Active TSS	Psoas Muscle	Psoas
48	chr2:11888200-11889400	Weak transcription	Fetal Heart	heart
49	chr2:11888200-11889800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:11888200-11890000	Flanking Active TSS	NHLF	lung

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