Variant report

Variant	rs12052800
Chromosome Location	chr2:40658936-40658937
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	SPI1	chr2:40658657-40659049	HL-60	blood:	n/a	chr2:40658725-40658732 chr2:40658856-40658869 chr2:40658857-40658870 chr2:40658859-40658868
2	GATA3	chr2:40658445-40659116	SK-N-SH	brain:	n/a	chr2:40659066-40659075
3	STAT3	chr2:40658661-40659015	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr2:40658748-40658986	MCF10A-Er-Src	breast:	n/a	chr2:40658928-40658939
5	MYC	chr2:40658768-40658956	MCF10A-Er-Src	breast:	n/a	n/a
6	NFIC	chr2:40658415-40659230	SK-N-SH	brain:	n/a	n/a
7	CTCF	chr2:40658860-40659010	AG10803	skin:	n/a	n/a
8	GATA2	chr2:40658033-40658970	SH-SY5Y	brain:	n/a	n/a
9	FOSL2	chr2:40658500-40659140	SK-N-SH	brain:	n/a	chr2:40658928-40658939
10	MYC	chr2:40658757-40658955	MCF10A-Er-Src	breast:	n/a	n/a
11	STAT3	chr2:40658713-40658937	MCF10A-Er-Src	breast:	n/a	n/a
12	STAT3	chr2:40658711-40659008	MCF10A-Er-Src	breast:	n/a	n/a
13	MAFK	chr2:40658629-40659023	IMR90	lung:	n/a	n/a
14	SPI1	chr2:40658701-40658996	GM12891	blood:	n/a	chr2:40658725-40658732 chr2:40658856-40658869 chr2:40658857-40658870 chr2:40658859-40658868
15	SPI1	chr2:40658511-40659176	HL-60	blood:	n/a	chr2:40658725-40658732 chr2:40658856-40658869 chr2:40658857-40658870 chr2:40658859-40658868
16	POLR2A	chr2:40658608-40659039	SK-N-SH	brain:	n/a	n/a
17	GATA3	chr2:40658029-40659242	SK-N-SH	brain:	n/a	chr2:40659066-40659075
18	FOS	chr2:40658671-40659008	MCF10A-Er-Src	breast:	n/a	chr2:40658928-40658939
19	CTCF	chr2:40658920-40659070	AoAF	blood vessel:	n/a	n/a
20	CTCF	chr2:40658920-40659070	HMF	breast:	n/a	n/a
21	FOS	chr2:40658724-40659012	MCF10A-Er-Src	breast:	n/a	chr2:40658928-40658939
22	TCF12	chr2:40657911-40659226	SK-N-SH	brain:	n/a	n/a
23	FOS	chr2:40658724-40658997	MCF10A-Er-Src	breast:	n/a	chr2:40658928-40658939
24	SPI1	chr2:40658728-40659056	GM12891	blood:	n/a	chr2:40658856-40658869 chr2:40658857-40658870 chr2:40658859-40658868
25	SPI1	chr2:40658715-40659032	GM12878	blood:	n/a	chr2:40658725-40658732 chr2:40658856-40658869 chr2:40658857-40658870 chr2:40658859-40658868
26	TCF12	chr2:40657962-40659153	SK-N-SH	brain:	n/a	n/a
27	CEBPB	chr2:40658650-40658961	IMR90	lung:	n/a	n/a
28	PBX3	chr2:40658569-40659093	SK-N-SH	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:40658891-40658941	HMEC	breast:	n/a
2	chr2:40658891-40658941	BE2_C	brain:	n/a
3	chr2:40658918-40658968	RPTEC	kidney:	n/a
4	chr2:40658891-40658941	SKMC	muscle:	n/a
5	chr2:40658918-40658968	HIPEpiC	eye:	n/a
6	chr2:40658891-40658941	GM12891	blood:	n/a
7	chr2:40658891-40658941	GM12892	blood:	n/a
8	chr2:40658918-40658968	AG09309	skin:	n/a
9	chr2:40658891-40658941	U87	brain:	n/a
10	chr2:40658918-40658968	MCF10A-Er-Src	breast:	n/a
11	chr2:40658891-40658941	Caco-2	colon:	n/a
12	chr2:40658918-40658968	AG04450	lung:	fetal
13	chr2:40658891-40658941	SAEC	small airway:	n/a
14	chr2:40658891-40658941	NHBE	bronchial:	n/a
15	chr2:40658891-40658941	LNCaP	prostate:	n/a
16	chr2:40658918-40658968	Jurkat	blood:	n/a
17	chr2:40658891-40658941	A549	lung:	n/a
18	chr2:40658918-40658968	HUVEC	blood vessel:	n/a
19	chr2:40658918-40658968	AoSMC	blood vessel:	n/a
20	chr2:40658891-40658941	HAEpiC	amniotic membrane:	n/a
21	chr2:40658891-40658941	HCF	heart:	n/a
22	chr2:40658891-40658941	HRCEpiC	kidney:	n/a
23	chr2:40658918-40658968	HAEpiC	amniotic membrane:	n/a
24	chr2:40658918-40658968	HRE	kidney:	n/a
25	chr2:40658891-40658941	HUVEC	blood vessel:	n/a
26	chr2:40658891-40658941	AG04449	skin:	fetal
27	chr2:40658918-40658968	IMR90	lung:	fetal
28	chr2:40658891-40658941	AG10803	skin:	n/a
29	chr2:40658918-40658968	HRCEpiC	kidney:	n/a
30	chr2:40658891-40658941	RPTEC	kidney:	n/a
31	chr2:40658918-40658968	NH-A	brain:	n/a
32	chr2:40658918-40658968	PFSK-1	brain:	n/a
33	chr2:40658891-40658941	HPAEpiC	pulmonary alveolar:	n/a
34	chr2:40658891-40658941	CMK	blood:	n/a
35	chr2:40658918-40658968	GM12878	blood:	n/a
36	chr2:40658891-40658941	HEK293	kidney:	embryo
37	chr2:40658918-40658968	K562	blood:	n/a
38	chr2:40658918-40658968	NT2-D1	testis:	n/a
39	chr2:40658918-40658968	GM12891	blood:	n/a
40	chr2:40658891-40658941	HRE	kidney:	n/a
41	chr2:40658918-40658968	U87	brain:	n/a
42	chr2:40658891-40658941	HRPEpiC	eye:	n/a
43	chr2:40658891-40658941	ProgFib	skin:	n/a
44	chr2:40658918-40658968	SK-N-SH	brain:	n/a
45	chr2:40658891-40658941	PFSK-1	brain:	n/a
46	chr2:40658891-40658941	PANC-1	pancreas:	n/a
47	chr2:40658918-40658968	AG10803	skin:	n/a
48	chr2:40658891-40658941	AG09319	gingival:	n/a
49	chr2:40658918-40658968	GM12892	blood:	n/a
50	chr2:40658891-40658941	HIPEpiC	eye:	n/a

Variant related genes	Relation type
SLC8A1	TF binding region
SLC8A1	CpG island

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10205556	0.85[CHB][hapmap]
rs11685475	0.92[ASN][1000 genomes]
rs11901878	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs12052649	0.95[CHB][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12052650	0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12105764	0.85[CHB][hapmap]
rs12988659	0.87[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13017237	0.87[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13023706	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13031785	0.81[TSI][hapmap]
rs13031843	0.81[TSI][hapmap]
rs13031849	0.81[TSI][hapmap]
rs13035085	0.81[TSI][hapmap]
rs13414307	0.80[CHB][hapmap]
rs13418726	0.85[CHB][hapmap]
rs17025965	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17025994	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17026012	0.81[TSI][hapmap]
rs2888677	0.80[CHB][hapmap]
rs2888678	0.80[CHB][hapmap]
rs34528721	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35129449	0.96[ASN][1000 genomes]
rs4366950	0.84[CHB][hapmap]
rs4629203	0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs4952621	0.95[CHB][hapmap];0.92[CHD][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs4952624	0.87[LWK][hapmap];1.00[MKK][hapmap]
rs4993292	0.81[TSI][hapmap]
rs6712702	0.89[JPT][hapmap]
rs6737011	0.85[CHB][hapmap]
rs6742589	0.91[ASN][1000 genomes]
rs7579930	0.88[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap];0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9789737	0.87[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9789739	0.87[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[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	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2757794	chr2:40547947-40733776	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2759044	chr2:40547947-40733776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40646600-40670800	Weak transcription	Fetal Brain Female	brain
2	chr2:40647600-40662200	Weak transcription	Brain Germinal Matrix	brain
3	chr2:40648000-40667200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:40648200-40676400	Weak transcription	Fetal Kidney	kidney
5	chr2:40653000-40674800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:40654200-40662200	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:40655000-40665000	Weak transcription	Fetal Brain Male	brain
8	chr2:40655400-40659800	Strong transcription	Dnd41	blood
9	chr2:40657000-40671200	Weak transcription	Fetal Stomach	stomach
10	chr2:40657200-40660600	Enhancers	Rectal Smooth Muscle	rectum
11	chr2:40657200-40662000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:40657400-40659800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr2:40657600-40659400	Enhancers	Fetal Heart	heart
14	chr2:40657800-40659200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:40657800-40663000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:40657800-40666600	Enhancers	Colon Smooth Muscle	Colon
17	chr2:40658000-40659000	Enhancers	Right Ventricle	heart
18	chr2:40658000-40659400	Enhancers	HSMM	muscle
19	chr2:40658000-40660800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr2:40658000-40663600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:40658000-40664000	Enhancers	NHDF-Ad	bronchial
22	chr2:40658000-40664200	Enhancers	HMEC	breast
23	chr2:40658200-40659000	Enhancers	Fetal Muscle Trunk	muscle
24	chr2:40658200-40659200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:40658200-40659200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:40658200-40659200	Enhancers	Brain Anterior Caudate	brain
27	chr2:40658200-40659200	Enhancers	Right Atrium	heart
28	chr2:40658200-40660000	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr2:40658200-40660000	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr2:40658200-40660000	Enhancers	Left Ventricle	heart
31	chr2:40658200-40660400	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr2:40658200-40661800	Enhancers	HSMMtube	muscle
33	chr2:40658200-40662200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:40658200-40663400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:40658200-40663600	Enhancers	Osteobl	bone
36	chr2:40658200-40665400	Enhancers	NHLF	lung
37	chr2:40658400-40659200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:40658400-40659200	Enhancers	Fetal Muscle Leg	muscle
39	chr2:40658400-40659600	Enhancers	NH-A	brain
40	chr2:40658400-40660000	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr2:40658400-40661400	Enhancers	Stomach Smooth Muscle	stomach
42	chr2:40658400-40663600	Enhancers	Adipose Nuclei	Adipose
43	chr2:40658600-40659000	Enhancers	HUVEC	blood vessel
44	chr2:40658600-40659200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:40658600-40659200	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr2:40658600-40659200	Enhancers	Fetal Intestine Small	intestine
47	chr2:40658600-40661800	Enhancers	NHEK	skin
48	chr2:40658600-40663400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr2:40658600-40663800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:40658800-40659000	Enhancers	Muscle Satellite Cultured Cells	--

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