Variant report

Variant	rs11124578
Chromosome Location	chr2:37549604-37549605
allele	A/C
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	EP300	chr2:37549491-37549814	SK-N-SH_RA	brain:	n/a	n/a
2	EP300	chr2:37548191-37553289	SK-N-SH	brain:	n/a	chr2:37553241-37553251 chr2:37551667-37551676 chr2:37551721-37551730 chr2:37552888-37552902 chr2:37552886-37552900 chr2:37548375-37548385 chr2:37552046-37552062 chr2:37551718-37551727 chr2:37551670-37551686 chr2:37551556-37551565 chr2:37549996-37550004 chr2:37551763-37551772 chr2:37552050-37552059 chr2:37552050-37552066 chr2:37551559-37551568 chr2:37551670-37551679 chr2:37551760-37551769 chr2:37551766-37551775
3	POLR2A	chr2:37549440-37549866	SK-N-SH	brain:	n/a	n/a
4	RCOR1	chr2:37549524-37549747	K562	blood:	n/a	n/a
5	EP300	chr2:37549487-37549821	SK-N-SH_RA	brain:	n/a	n/a
6	RCOR1	chr2:37549515-37549934	K562	blood:	n/a	n/a
7	MXI1	chr2:37547850-37553154	SK-N-SH	brain:	n/a	n/a
8	EP300	chr2:37549599-37549762	K562	blood:	n/a	n/a
9	GATA3	chr2:37549334-37550145	SK-N-SH	brain:	n/a	n/a
10	TAL1	chr2:37549519-37549810	K562	blood:	n/a	chr2:37549621-37549639 chr2:37549712-37549727
11	JUN	chr2:37549420-37549844	K562	blood:	n/a	chr2:37549768-37549777 chr2:37549753-37549762
12	PBX3	chr2:37549507-37549967	SK-N-SH	brain:	n/a	chr2:37549767-37549776 chr2:37549754-37549763
13	RAD21	chr2:37549534-37549778	SK-N-SH_RA	brain:	n/a	n/a
14	NFYB	chr2:37549586-37549917	GM12878	blood:	n/a	chr2:37549753-37549768 chr2:37549754-37549764 chr2:37549753-37549766 chr2:37549764-37549779 chr2:37549764-37549779 chr2:37549751-37549766 chr2:37549766-37549776 chr2:37549764-37549778 chr2:37549751-37549766 chr2:37549752-37549766 chr2:37549754-37549764
15	GATA1	chr2:37549432-37550004	PBDE	blood:	n/a	n/a
16	GATA3	chr2:37549391-37550097	SK-N-SH	brain:	n/a	n/a
17	GATA3	chr2:37549583-37549790	T-47D	breast:	n/a	n/a
18	YY1	chr2:37549462-37549836	SK-N-SH_RA	brain:	n/a	n/a
19	GATA2	chr2:37549509-37549801	SH-SY5Y	brain:	n/a	n/a
20	NFYB	chr2:37549575-37549896	K562	blood:	n/a	chr2:37549753-37549768 chr2:37549754-37549764 chr2:37549753-37549766 chr2:37549764-37549779 chr2:37549764-37549779 chr2:37549751-37549766 chr2:37549766-37549776 chr2:37549764-37549778 chr2:37549751-37549766 chr2:37549752-37549766 chr2:37549754-37549764

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:37453426..37455818-chr2:37549364..37551378,2	K562	blood:
2	chr2:37466663..37469374-chr2:37548966..37550827,2	K562	blood:

Variant related genes	Relation type
PRKD3	TF binding region
ENSG00000232028	TF binding region
ENSG00000003509	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10177176	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs10190959	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs1056021	0.84[CHB][hapmap]
rs11124574	0.84[CHB][hapmap]
rs11124576	0.93[CEU][hapmap]
rs1158218	0.90[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs1158219	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs11682607	0.82[ASN][1000 genomes]
rs11689794	0.92[ASN][1000 genomes]
rs12616151	0.89[ASN][1000 genomes]
rs12618410	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs12712532	0.90[ASN][1000 genomes]
rs13015451	0.91[ASN][1000 genomes]
rs13030789	0.84[ASN][1000 genomes]
rs13420463	0.85[ASN][1000 genomes]
rs1477055	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[YRI][hapmap]
rs17020386	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17020490	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17409947	0.86[CEU][hapmap]
rs17481834	0.86[CEU][hapmap]
rs1989172	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2041836	0.83[CHB][hapmap]
rs2268987	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2300881	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2300884	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2302650	0.80[CEU][hapmap]
rs2372993	0.84[ASN][1000 genomes]
rs3770757	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3770759	0.85[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs3819892	0.86[CEU][hapmap]
rs4581878	0.85[ASN][1000 genomes]
rs4670194	0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4670195	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4670688	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4670689	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4998429	0.84[JPT][hapmap]
rs56774710	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs57361399	0.93[ASN][1000 genomes]
rs6544066	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs67467920	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs71398224	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs72792829	0.83[ASN][1000 genomes]
rs74177070	0.87[ASN][1000 genomes]
rs7563610	0.80[ASN][1000 genomes]
rs7568510	0.90[ASN][1000 genomes]
rs7570547	0.92[ASN][1000 genomes]
rs7584565	0.90[ASN][1000 genomes]
rs9309004	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs9318	0.83[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430724	chr2:37546820-37628704	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37484600-37550400	Weak transcription	Right Ventricle	heart
2	chr2:37509000-37550800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:37511000-37550800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:37520400-37550400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr2:37530600-37550400	Weak transcription	Thymus	Thymus
6	chr2:37533200-37550400	Weak transcription	Fetal Intestine Large	intestine
7	chr2:37534000-37550400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:37534400-37550400	Weak transcription	Lung	lung
9	chr2:37534400-37550600	Weak transcription	Left Ventricle	heart
10	chr2:37537000-37550400	Weak transcription	HSMMtube	muscle
11	chr2:37542000-37550400	Weak transcription	Colonic Mucosa	Colon
12	chr2:37542400-37550800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:37542800-37550800	Weak transcription	Gastric	stomach
14	chr2:37543000-37550400	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr2:37543600-37550400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:37543800-37550600	Weak transcription	Fetal Brain Male	brain
17	chr2:37545800-37550400	Weak transcription	Ovary	ovary
18	chr2:37546000-37550400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:37546000-37551000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr2:37546400-37550400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr2:37547200-37549800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:37547400-37550200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:37548000-37549800	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr2:37548200-37550400	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr2:37548200-37550400	Enhancers	Primary B cells from peripheral blood	blood
26	chr2:37548200-37550600	Enhancers	Primary B cells from cord blood	blood
27	chr2:37548200-37550800	Weak transcription	Stomach Mucosa	stomach
28	chr2:37548400-37549800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
29	chr2:37548400-37549800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:37548400-37549800	Enhancers	Fetal Kidney	kidney
31	chr2:37548400-37550000	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr2:37548400-37550200	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr2:37548400-37550200	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr2:37548400-37550200	Enhancers	HepG2	liver
35	chr2:37548400-37550400	Enhancers	Primary hematopoietic stem cells	blood
36	chr2:37548400-37550400	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr2:37548400-37550400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr2:37548400-37550400	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr2:37548400-37550400	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr2:37548400-37550400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr2:37548400-37550600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr2:37548400-37551000	Flanking Active TSS	Dnd41	blood
43	chr2:37548600-37550000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:37548600-37550000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:37548600-37550000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr2:37548600-37550000	Flanking Active TSS	NHEK	skin
47	chr2:37548600-37550400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr2:37548600-37550400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr2:37548600-37550400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr2:37548600-37550400	Enhancers	Liver	Liver

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