Variant report

Variant	rs12209087
Chromosome Location	chr6:121650512-121650513
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	chr6:121645992..121651624-chr6:121651961..121657811,7	K562	blood:

Variant related genes	Relation type
ENSG00000146350	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11154014	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1846865	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1891646	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1995313	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2038833	0.87[ASN][1000 genomes]
rs3956400	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4395765	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4412234	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4412244	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4461766	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4498397	0.83[ASN][1000 genomes]
rs4946562	0.85[EUR][1000 genomes]
rs4946565	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6569197	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569200	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6903298	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6911380	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6916050	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6919890	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6926502	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6928060	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6941235	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7450632	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7768058	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9320799	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9320801	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9320805	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9320806	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320807	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320808	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9372652	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9375004	0.81[AMR][1000 genomes]
rs9375019	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9375021	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9375022	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9385193	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9387929	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9387939	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9387942	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9398631	0.87[EUR][1000 genomes]
rs9401380	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9401382	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9401387	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9401388	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9482119	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9490184	0.83[ASN][1000 genomes]
rs9885676	0.86[ASN][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	nsv1023384	chr6:121235867-121683448	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv530527	chr6:121298528-121789855	ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv830789	chr6:121581450-121732320	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:121586400-121655000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr6:121588400-121655200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:121589000-121654200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:121589200-121655000	Weak transcription	Fetal Stomach	stomach
5	chr6:121594200-121654800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:121604800-121653000	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr6:121606600-121655000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:121611200-121655000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:121615600-121655000	Weak transcription	Pancreas	Pancrea
10	chr6:121616200-121655000	Weak transcription	Fetal Muscle Leg	muscle
11	chr6:121617200-121651600	Weak transcription	GM12878-XiMat	blood
12	chr6:121622200-121654600	Weak transcription	Fetal Thymus	thymus
13	chr6:121622600-121655000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:121622800-121654800	Weak transcription	Brain Germinal Matrix	brain
15	chr6:121630600-121651600	Weak transcription	K562	blood
16	chr6:121632000-121654200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:121632200-121653800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr6:121632200-121654200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr6:121632200-121655000	Weak transcription	HSMM	muscle
20	chr6:121632400-121654600	Weak transcription	HMEC	breast
21	chr6:121632800-121655000	Weak transcription	Lung	lung
22	chr6:121634600-121654800	Weak transcription	Fetal Brain Male	brain
23	chr6:121635000-121653800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr6:121635200-121655200	Weak transcription	Aorta	Aorta
25	chr6:121636000-121654800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr6:121636200-121654200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr6:121636600-121655000	Weak transcription	Esophagus	oesophagus
28	chr6:121636800-121654800	Weak transcription	Placenta	Placenta
29	chr6:121637000-121655000	Weak transcription	Fetal Intestine Small	intestine
30	chr6:121637200-121654000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr6:121637200-121655000	Weak transcription	Liver	Liver
32	chr6:121637600-121651400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:121638200-121651600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr6:121638200-121655200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:121638400-121654400	Weak transcription	Primary B cells from peripheral blood	blood
36	chr6:121638800-121654400	Weak transcription	Primary T cells from cord blood	blood
37	chr6:121639600-121651400	Weak transcription	Dnd41	blood
38	chr6:121639600-121654400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:121640600-121654200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr6:121640600-121654200	Weak transcription	Fetal Intestine Large	intestine
41	chr6:121640600-121654800	Weak transcription	Brain Angular Gyrus	brain
42	chr6:121640600-121655200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr6:121640600-121655200	Weak transcription	Adipose Nuclei	Adipose
44	chr6:121640600-121655200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr6:121640600-121655200	Weak transcription	NH-A	brain
46	chr6:121640600-121655400	Weak transcription	Fetal Heart	heart
47	chr6:121640800-121651600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:121640800-121654200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:121640800-121654600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr6:121640800-121654600	Weak transcription	Small Intestine	intestine

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