Variant report

Variant	rs1554693
Chromosome Location	chr12:47586280-47586281
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:47579082..47584431-chr12:47584905..47587812,5	K562	blood:
2	chr12:47498470..47501746-chr12:47583705..47586367,3	MCF-7	breast:
3	chr12:47583159..47586380-chr12:47586604..47590176,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263838	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10785664	1.00[YRI][hapmap]
rs10785665	1.00[YRI][hapmap]
rs10785668	1.00[YRI][hapmap]
rs10881069	1.00[YRI][hapmap]
rs10881070	1.00[YRI][hapmap]
rs10881077	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10881079	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11183738	1.00[YRI][hapmap]
rs11183750	1.00[YRI][hapmap]
rs11183752	1.00[YRI][hapmap]
rs11183777	1.00[YRI][hapmap]
rs11183779	1.00[CHB][hapmap]
rs11183783	1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs11183795	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183796	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183799	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12368600	1.00[YRI][hapmap]
rs12370622	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17821774	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17822189	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1917657	1.00[YRI][hapmap]
rs2004683	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2004684	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2111903	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2408718	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4768142	1.00[YRI][hapmap]
rs4768143	1.00[YRI][hapmap]
rs4768144	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4768779	1.00[YRI][hapmap]
rs4768781	1.00[YRI][hapmap]
rs4768782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55711758	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55849521	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs712100	1.00[CHB][hapmap]
rs73110240	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs732523	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7974410	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855146	1.00[CHB][hapmap]
rs855147	1.00[CHB][hapmap]
rs873935	1.00[CHB][hapmap]

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	nsv469368	chr12:47374908-47675680	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv558784	chr12:47374908-47675680	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv832399	chr12:47502910-47689601	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2751100	chr12:47541390-47746157	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47578200-47587800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:47581800-47594000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr12:47583200-47587200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr12:47583200-47587600	Weak transcription	Pancreas	Pancrea
5	chr12:47583200-47588400	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr12:47583200-47589200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:47583200-47628600	Weak transcription	Aorta	Aorta
8	chr12:47583400-47588000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:47583400-47588400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr12:47583800-47587600	Weak transcription	Lung	lung
11	chr12:47584000-47600600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:47584200-47587000	Weak transcription	Psoas Muscle	Psoas
13	chr12:47584200-47587600	Weak transcription	Right Atrium	heart
14	chr12:47584200-47589600	Enhancers	Primary B cells from peripheral blood	blood
15	chr12:47584600-47586600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:47584600-47587000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:47584600-47587000	Weak transcription	Spleen	Spleen
18	chr12:47584600-47587200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr12:47584600-47587400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr12:47584600-47587600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:47584600-47588400	Weak transcription	Adipose Nuclei	Adipose
22	chr12:47584800-47586400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr12:47584800-47586400	Weak transcription	K562	blood
24	chr12:47584800-47586600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr12:47584800-47586800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr12:47584800-47587000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:47584800-47597200	Weak transcription	Primary B cells from cord blood	blood
28	chr12:47584800-47605800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:47585000-47586400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr12:47585000-47587000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:47585000-47587000	Weak transcription	NH-A	brain
32	chr12:47585000-47588600	Enhancers	GM12878-XiMat	blood
33	chr12:47585200-47586600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr12:47585200-47586600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr12:47585200-47586600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr12:47585200-47586600	Enhancers	Small Intestine	intestine
37	chr12:47585200-47587400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr12:47585200-47587800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr12:47585400-47586800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
40	chr12:47585400-47587000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:47585400-47587000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:47585400-47587200	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr12:47585400-47587600	Weak transcription	Left Ventricle	heart
44	chr12:47585400-47587800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr12:47585400-47590200	Enhancers	A549	lung
46	chr12:47585400-47592800	Weak transcription	NHEK	skin
47	chr12:47585400-47600400	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr12:47585600-47586600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr12:47585600-47586600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:47585600-47588600	Enhancers	Liver	Liver

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