Variant report

Variant	rs12090303
Chromosome Location	chr1:220186731-220186732
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:220173071..220175187-chr1:220185418..220188228,2	K562	blood:
2	chr1:220186134..220187962-chr1:220260106..220262494,2	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11118488	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11811749	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12057663	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12059479	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12059527	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12060231	0.96[AFR][1000 genomes]
rs12072662	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12079635	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12080610	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12080935	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12084196	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12095669	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5030751	0.96[AFR][1000 genomes]
rs6690280	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6692978	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6702241	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	nsv427930	chr1:220120379-220333434	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	744 gene(s)	inside rSNPs	diseases
2	nsv998124	chr1:220132739-220189211	Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	n/a
3	nsv832636	chr1:220139697-220294352	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	738 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	chr1:220140800-220192400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:220141200-220192200	Weak transcription	Fetal Kidney	kidney
3	chr1:220164800-220200200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr1:220165800-220200200	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr1:220166000-220189200	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr1:220166000-220198800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:220166200-220199200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:220166200-220200200	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr1:220166200-220208400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:220166200-220209000	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr1:220166400-220199800	Strong transcription	K562	blood
12	chr1:220166400-220200200	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:220166400-220206800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:220166400-220210600	Strong transcription	Duodenum Mucosa	Duodenum
15	chr1:220166600-220188400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:220166600-220200400	Strong transcription	Primary B cells from peripheral blood	blood
17	chr1:220166800-220199000	Strong transcription	Dnd41	blood
18	chr1:220166800-220208400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:220167200-220200200	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:220167800-220211800	Weak transcription	Stomach Mucosa	stomach
21	chr1:220168400-220213800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:220169200-220206400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:220170400-220218600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:220172600-220218600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:220174200-220188400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:220174400-220187800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:220174400-220198600	Strong transcription	Primary T cells from cord blood	blood
28	chr1:220176000-220187200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:220176000-220188200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:220176000-220208000	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:220176200-220189400	Strong transcription	HMEC	breast
32	chr1:220176200-220194200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:220176400-220208400	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr1:220176600-220200200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr1:220177600-220197800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:220177600-220205800	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr1:220178000-220187800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:220178000-220190800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:220178000-220195400	Weak transcription	Gastric	stomach
40	chr1:220178000-220197400	Weak transcription	Fetal Brain Male	brain
41	chr1:220178000-220217800	Weak transcription	Pancreas	Pancrea
42	chr1:220178200-220192400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr1:220178200-220218600	Weak transcription	Right Ventricle	heart
44	chr1:220179000-220191800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr1:220179200-220192400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr1:220179600-220192200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr1:220180600-220190200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr1:220180800-220190800	Weak transcription	Colon Smooth Muscle	Colon
49	chr1:220181200-220188400	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr1:220181200-220191000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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