Variant report

Variant	rs12924889
Chromosome Location	chr16:12241768-12241769
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:12241354..12243525-chr16:12245349..12247031,2	K562	blood:
2	chr16:12240782..12243525-chr16:12245349..12247044,3	K562	blood:
3	chr16:12235799..12238230-chr16:12240005..12241977,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11075049	0.82[JPT][hapmap]
rs11075054	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11639556	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11642033	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11642386	0.87[JPT][hapmap]
rs11646458	0.85[ASN][1000 genomes]
rs11646539	0.92[ASN][1000 genomes]
rs11646584	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11647572	0.93[ASN][1000 genomes]
rs11648468	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs11648816	0.87[JPT][hapmap]
rs12443524	0.80[EUR][1000 genomes]
rs12596703	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12599107	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12599793	0.93[ASN][1000 genomes]
rs12708747	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12926900	0.87[JPT][hapmap]
rs12929519	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13333662	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs13336687	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs16958964	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs2136250	0.91[ASN][1000 genomes]
rs2175020	0.92[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34098770	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34147612	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34565142	0.93[EUR][1000 genomes]
rs34598762	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35208076	0.92[EUR][1000 genomes]
rs35293822	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35542345	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3851011	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs3851012	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs3851013	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3851014	0.91[ASN][1000 genomes]
rs3862466	0.89[ASN][1000 genomes]
rs3893358	0.89[ASN][1000 genomes]
rs3894905	1.00[ASW][hapmap]
rs4781180	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs8048589	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs8050180	0.82[JPT][hapmap]
rs8063329	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs9935284	0.93[ASN][1000 genomes]
rs9936270	0.93[ASN][1000 genomes]
rs9939383	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1052973	chr16:12188092-12307880	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1042146	chr16:12208242-12256699	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1039590	chr16:12237623-12279574	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12213800-12255400	Weak transcription	Gastric	stomach
2	chr16:12217800-12241800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr16:12227600-12247000	Weak transcription	Colon Smooth Muscle	Colon
4	chr16:12228600-12243600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr16:12229000-12249000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr16:12229400-12242800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr16:12229400-12248000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr16:12229400-12250600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr16:12229800-12244400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr16:12229800-12251400	Weak transcription	NHEK	skin
11	chr16:12229800-12253600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr16:12230000-12245600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr16:12230200-12241800	Weak transcription	Esophagus	oesophagus
14	chr16:12230200-12242000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr16:12230200-12256200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr16:12231400-12251000	Weak transcription	Ovary	ovary
17	chr16:12231400-12268000	Weak transcription	Pancreas	Pancrea
18	chr16:12232000-12248600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr16:12233600-12251000	Weak transcription	NHDF-Ad	bronchial
20	chr16:12234600-12244000	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr16:12234600-12247600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr16:12234600-12248600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr16:12234600-12261600	Weak transcription	Aorta	Aorta
24	chr16:12234600-12265600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr16:12235400-12251000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr16:12235800-12243400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr16:12236200-12243000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr16:12236200-12243800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr16:12236200-12249400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr16:12236200-12250800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr16:12237600-12241800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr16:12237600-12243400	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr16:12237800-12249600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr16:12239000-12242600	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr16:12239800-12242400	Enhancers	H1 Cell Line	embryonic stem cell
36	chr16:12239800-12243400	Enhancers	Fetal Muscle Leg	muscle
37	chr16:12240200-12242200	Enhancers	HSMMtube	muscle
38	chr16:12240400-12242400	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr16:12240400-12242600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr16:12240600-12242200	Enhancers	Primary B cells from peripheral blood	blood
41	chr16:12240800-12242200	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr16:12240800-12242200	Enhancers	Brain Germinal Matrix	brain
43	chr16:12240800-12242200	Enhancers	HSMM	muscle
44	chr16:12240800-12242400	Enhancers	Primary hematopoietic stem cells	blood
45	chr16:12240800-12242400	Enhancers	Brain Hippocampus Middle	brain
46	chr16:12240800-12242400	Enhancers	Fetal Brain Male	brain
47	chr16:12240800-12243000	Enhancers	Primary T cells fromperipheralblood	blood
48	chr16:12240800-12243600	Enhancers	Fetal Heart	heart
49	chr16:12241000-12241800	Enhancers	Primary B cells from cord blood	blood
50	chr16:12241000-12241800	Enhancers	Skeletal Muscle Female	skeletal muscle

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