Variant report

Variant	rs2029686
Chromosome Location	chr12:51564802-51564803
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:51564751..51566966-chr12:51783543..51785825,2	K562	blood:
2	chr12:51474365..51478814-chr12:51563597..51568148,9	K562	blood:
3	chr12:51564447..51569582-chr12:51630930..51635335,8	K562	blood:
4	chr12:51557800..51560128-chr12:51563372..51565944,2	K562	blood:
5	chr12:51563450..51568971-chr12:51609008..51613972,14	K562	blood:
6	chr12:51557800..51560550-chr12:51563372..51565178,2	K562	blood:
7	chr12:51474365..51480004-chr12:51564069..51568503,12	K562	blood:
8	chr12:51564257..51569582-chr12:51630930..51636873,13	K562	blood:

No data

Variant related genes	Relation type
ENSG00000183283	Chromatin interaction
ENSG00000050438	Chromatin interaction
ENSG00000139629	Chromatin interaction
ENSG00000110925	Chromatin interaction
ENSG00000184271	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10099	0.90[JPT][hapmap]
rs1038526	0.90[JPT][hapmap]
rs10783414	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10783416	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10783417	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10783418	1.00[ASW][hapmap];0.91[CEU][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10876143	0.87[EUR][1000 genomes]
rs10876146	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1565721	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1984544	0.87[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1985457	0.82[EUR][1000 genomes]
rs2436645	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2436646	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2436647	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2640511	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2640516	0.90[JPT][hapmap]
rs2640521	0.86[EUR][1000 genomes]
rs2640523	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2640527	0.83[ASN][1000 genomes]
rs2730647	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2730648	0.95[JPT][hapmap]
rs2730650	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2730654	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2956428	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6580799	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6580800	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6580801	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6580803	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6580804	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7306522	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7959378	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51513000-51565400	Weak transcription	Fetal Lung	lung
2	chr12:51519000-51565000	Weak transcription	Colon Smooth Muscle	Colon
3	chr12:51519000-51565200	Weak transcription	Left Ventricle	heart
4	chr12:51519000-51565200	Weak transcription	Pancreas	Pancrea
5	chr12:51519000-51565800	Weak transcription	Esophagus	oesophagus
6	chr12:51519200-51565000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr12:51519400-51565200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr12:51521600-51565200	Weak transcription	HSMM	muscle
9	chr12:51527400-51565200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:51532000-51565000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr12:51532600-51565200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:51533600-51565000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:51539600-51565000	Weak transcription	Primary B cells from peripheral blood	blood
14	chr12:51543200-51565200	Weak transcription	Psoas Muscle	Psoas
15	chr12:51545000-51565000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:51545000-51565000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr12:51550400-51565400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:51552400-51565000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr12:51553200-51565000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:51554400-51565000	Weak transcription	HUVEC	blood vessel
21	chr12:51554800-51565000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr12:51554800-51565000	Weak transcription	NHLF	lung
23	chr12:51554800-51565200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:51554800-51565400	Weak transcription	Brain Anterior Caudate	brain
25	chr12:51555200-51565000	Weak transcription	Brain Substantia Nigra	brain
26	chr12:51555400-51565200	Weak transcription	Thymus	Thymus
27	chr12:51556000-51565200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr12:51557000-51565000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr12:51557200-51565000	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr12:51559000-51565000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:51559400-51565000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr12:51560400-51565200	Weak transcription	Lung	lung
33	chr12:51560600-51565000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr12:51560600-51565000	Weak transcription	NHEK	skin
35	chr12:51560600-51565200	Weak transcription	Right Ventricle	heart
36	chr12:51560600-51565600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:51560600-51565600	Weak transcription	Gastric	stomach
38	chr12:51561000-51565200	Weak transcription	Right Atrium	heart
39	chr12:51561200-51565400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr12:51561200-51565400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr12:51561600-51565200	Enhancers	Primary T cells fromperipheralblood	blood
42	chr12:51561800-51565000	Weak transcription	Primary B cells from cord blood	blood
43	chr12:51561800-51565200	Weak transcription	Fetal Thymus	thymus
44	chr12:51562200-51565200	Weak transcription	Ovary	ovary
45	chr12:51562400-51565200	Weak transcription	Spleen	Spleen
46	chr12:51562600-51565000	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr12:51562800-51565400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr12:51563200-51565600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:51563400-51565600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr12:51563600-51565000	Enhancers	Primary T helper cells PMA-I stimulated	--

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