Variant report

Variant	rs11168424
Chromosome Location	chr12:48527715-48527716
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48523386..48526206-chr12:48526341..48529296,3	K562	blood:
2	chr12:48527054..48529468-chr12:48538732..48540822,3	K562	blood:
3	chr12:48525679..48529309-chr12:48532044..48535896,3	K562	blood:

Variant related genes	Relation type
ENSG00000152556	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10492081	0.82[YRI][hapmap]
rs10492082	0.80[EUR][1000 genomes]
rs1049392	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10747529	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10875733	0.87[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.86[EUR][1000 genomes]
rs10875739	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10875741	0.89[ASN][1000 genomes]
rs10875744	0.91[ASN][1000 genomes]
rs10875752	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10875754	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10875759	0.85[CHB][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10875761	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10875766	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11168350	0.93[JPT][hapmap]
rs11168353	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs11168354	1.00[JPT][hapmap]
rs11168358	1.00[JPT][hapmap]
rs11168363	0.81[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs11168364	0.81[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs11168373	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[EUR][1000 genomes]
rs11168378	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11168404	0.87[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168412	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168419	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11168435	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11168438	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11168439	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11168442	0.85[AMR][1000 genomes]
rs11168443	0.83[AMR][1000 genomes]
rs11168444	0.85[AMR][1000 genomes]
rs11168445	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs11168446	0.85[AMR][1000 genomes]
rs11168447	0.85[AMR][1000 genomes]
rs11168448	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs11168453	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[AMR][1000 genomes]
rs11168454	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs11832455	0.81[ASN][1000 genomes]
rs11834818	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12228924	0.90[CEU][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12422355	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[EUR][1000 genomes]
rs12423250	0.94[JPT][hapmap]
rs12425679	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12426981	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs17122567	0.92[GIH][hapmap];1.00[JPT][hapmap]
rs1859443	0.93[JPT][hapmap]
rs1978161	0.81[JPT][hapmap]
rs2107640	0.81[ASN][1000 genomes]
rs2158515	0.91[ASN][1000 genomes]
rs2240306	0.85[EUR][1000 genomes]
rs2286020	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2291483	0.88[MEX][hapmap]
rs2408954	1.00[JPT][hapmap]
rs3742075	0.89[CHB][hapmap];0.93[JPT][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3825403	1.00[JPT][hapmap]
rs4258439	1.00[JPT][hapmap]
rs56097189	0.81[ASN][1000 genomes]
rs56129148	0.84[ASN][1000 genomes]
rs57430775	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58540891	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58556309	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59537300	0.85[AMR][1000 genomes]
rs59667534	0.81[EUR][1000 genomes]
rs6580658	0.89[CHB][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes]
rs66507954	0.85[AMR][1000 genomes]
rs7132898	0.85[ASN][1000 genomes]
rs7133274	0.80[AMR][1000 genomes]
rs7136243	0.85[AMR][1000 genomes]
rs7136782	0.83[AMR][1000 genomes]
rs7136788	0.85[AMR][1000 genomes]
rs7299704	1.00[JPT][hapmap]
rs7302354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7303677	0.87[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7304428	0.89[ASN][1000 genomes]
rs73104071	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73304926	0.85[AMR][1000 genomes]
rs7484942	0.83[CEU][hapmap];0.89[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs765260	1.00[JPT][hapmap]
rs7962390	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[AMR][1000 genomes]
rs7962569	0.89[CHB][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes]
rs8181670	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs886589	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs954326	0.94[JPT][hapmap]
rs9651981	0.96[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs9804751	0.96[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer 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	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48514000-48536600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr12:48514000-48537200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:48515600-48535600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr12:48515800-48535600	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:48515800-48545600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:48516200-48529600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr12:48516200-48545400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:48516200-48547200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:48516400-48529400	Strong transcription	Ovary	ovary
10	chr12:48516400-48529600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:48516400-48535600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:48516400-48535800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:48516400-48542000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr12:48516400-48545000	Strong transcription	GM12878-XiMat	blood
15	chr12:48516400-48545400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr12:48516400-48545800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:48516400-48547200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:48516400-48547200	Strong transcription	Stomach Smooth Muscle	stomach
19	chr12:48516400-48547800	Strong transcription	Fetal Stomach	stomach
20	chr12:48516600-48527800	Weak transcription	Small Intestine	intestine
21	chr12:48516600-48536600	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr12:48516600-48543200	Weak transcription	Stomach Mucosa	stomach
23	chr12:48516600-48545400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:48516600-48545600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:48516800-48529400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr12:48516800-48530400	Strong transcription	Osteobl	bone
27	chr12:48516800-48547400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:48517200-48529600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:48517600-48547400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:48518200-48529800	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr12:48518600-48547600	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr12:48519000-48527800	Weak transcription	Fetal Thymus	thymus
33	chr12:48519600-48547200	Strong transcription	Primary B cells from peripheral blood	blood
34	chr12:48519800-48529800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:48520000-48529400	Strong transcription	NHEK	skin
36	chr12:48520000-48545600	Strong transcription	Hela-S3	cervix
37	chr12:48520600-48529400	Strong transcription	Fetal Muscle Trunk	muscle
38	chr12:48520600-48529600	Strong transcription	HSMM	muscle
39	chr12:48520600-48529800	Strong transcription	Brain Germinal Matrix	brain
40	chr12:48520800-48547400	Strong transcription	Fetal Brain Female	brain
41	chr12:48521000-48529400	Strong transcription	Brain Anterior Caudate	brain
42	chr12:48521400-48529600	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr12:48522000-48529400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:48522400-48534400	Weak transcription	NHDF-Ad	bronchial
45	chr12:48522600-48529400	Strong transcription	Aorta	Aorta
46	chr12:48522600-48529600	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr12:48522600-48532800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:48522800-48530200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr12:48523000-48529400	Strong transcription	Fetal Lung	lung
50	chr12:48523200-48529200	Strong transcription	Primary T cells from cord blood	blood

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