Variant report

Variant	rs3951438
Chromosome Location	chr12:51658609-51658610
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	chr12:51651947..51654045-chr12:51655444..51659174,3	K562	blood:
2	chr12:51658184..51660274-chr12:51733778..51735476,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10747609	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10783426	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10783427	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10783428	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10876157	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10876159	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1877260	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1877261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1975004	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2271821	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2359449	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2884709	0.92[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3886185	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4761814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4761815	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4761935	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4761938	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4761966	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4761969	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4761981	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4761995	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6580820	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7133495	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7136290	0.80[AMR][1000 genomes]
rs7296747	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7304578	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7311434	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7316347	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7316569	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7957667	0.80[AMR][1000 genomes]
rs9325148	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv482304	chr12:51653496-51814917	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 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	chr12:51638400-51662800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:51639800-51662800	Weak transcription	Fetal Stomach	stomach
3	chr12:51640200-51662800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr12:51640200-51662800	Weak transcription	Pancreas	Pancrea
5	chr12:51640400-51659000	Weak transcription	HMEC	breast
6	chr12:51640400-51661600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr12:51640600-51661800	Weak transcription	NH-A	brain
8	chr12:51641600-51663000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:51642000-51662800	Weak transcription	NHLF	lung
10	chr12:51642200-51661000	Weak transcription	Colonic Mucosa	Colon
11	chr12:51642200-51662800	Weak transcription	Gastric	stomach
12	chr12:51642200-51662800	Weak transcription	Right Ventricle	heart
13	chr12:51642200-51663000	Weak transcription	Lung	lung
14	chr12:51642400-51659400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:51642400-51662800	Weak transcription	Primary B cells from cord blood	blood
16	chr12:51642600-51659200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr12:51642600-51659800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr12:51642600-51662600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr12:51642800-51658800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr12:51643000-51662600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr12:51643200-51662800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr12:51644800-51659200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:51645000-51658800	Weak transcription	Dnd41	blood
24	chr12:51645200-51661800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:51647800-51659200	Weak transcription	Placenta	Placenta
26	chr12:51648800-51662600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr12:51649400-51661400	Weak transcription	Esophagus	oesophagus
28	chr12:51649400-51662800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr12:51649600-51659400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:51651000-51662800	Weak transcription	Liver	Liver
31	chr12:51651200-51659200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr12:51651200-51660200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr12:51651400-51662800	Weak transcription	Fetal Intestine Large	intestine
34	chr12:51653400-51663400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:51654200-51662800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr12:51656600-51659000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr12:51656800-51659000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr12:51656800-51660000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr12:51656800-51662800	Weak transcription	Ovary	ovary
40	chr12:51656800-51662800	Weak transcription	Spleen	Spleen
41	chr12:51657000-51658800	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr12:51657000-51659000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr12:51657000-51659000	Weak transcription	K562	blood
44	chr12:51657000-51660800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr12:51657000-51661600	Weak transcription	Duodenum Mucosa	Duodenum
46	chr12:51657000-51662200	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr12:51657000-51662800	Weak transcription	Adipose Nuclei	Adipose
48	chr12:51657000-51662800	Weak transcription	A549	lung
49	chr12:51657200-51662800	Weak transcription	Hela-S3	cervix
50	chr12:51657400-51660000	Weak transcription	Muscle Satellite Cultured Cells	--

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