Variant report

Variant	rs55893407
Chromosome Location	chr12:104386311-104386312
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104384261..104388673-chr12:104456948..104460032,3	K562	blood:
2	chr12:104369091..104370992-chr12:104385433..104387266,2	K562	blood:

Variant related genes	Relation type
ENSG00000120820	Chromatin interaction
ENSG00000111727	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10778307	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11553765	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12426382	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17034946	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17034960	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17035056	0.80[ASN][1000 genomes]
rs17035129	0.95[AMR][1000 genomes]
rs1882019	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2293626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2629805	0.98[ASN][1000 genomes]
rs2722200	0.90[ASN][1000 genomes]
rs2888805	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3751207	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3751208	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3829300	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4135060	0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4135065	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4135076	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4135078	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4135082	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4135085	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4135086	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4135087	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4135094	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4135095	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4135118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4135131	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4135150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55780086	0.85[EUR][1000 genomes]
rs55871448	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60534873	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73390446	0.85[AMR][1000 genomes];0.85[EUR][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	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104362000-104392800	Weak transcription	Fetal Brain Male	brain
2	chr12:104377800-104390200	Weak transcription	Fetal Heart	heart
3	chr12:104377800-104391000	Weak transcription	Colon Smooth Muscle	Colon
4	chr12:104377800-104400200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:104379600-104387000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr12:104380600-104388000	Weak transcription	NHEK	skin
7	chr12:104380800-104386400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr12:104380800-104386400	Weak transcription	Fetal Stomach	stomach
9	chr12:104380800-104386600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:104380800-104387000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:104380800-104387200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:104380800-104387200	Weak transcription	Brain Hippocampus Middle	brain
13	chr12:104380800-104387800	Weak transcription	HSMMtube	muscle
14	chr12:104380800-104388200	Weak transcription	Psoas Muscle	Psoas
15	chr12:104380800-104391400	Weak transcription	Ovary	ovary
16	chr12:104380800-104395600	Weak transcription	Aorta	Aorta
17	chr12:104380800-104400200	Weak transcription	NHLF	lung
18	chr12:104381000-104386400	Weak transcription	Fetal Kidney	kidney
19	chr12:104381000-104386600	Weak transcription	Brain Anterior Caudate	brain
20	chr12:104381000-104386600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr12:104381000-104387000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr12:104381000-104387200	Weak transcription	Primary B cells from peripheral blood	blood
23	chr12:104381000-104387400	Weak transcription	Brain Germinal Matrix	brain
24	chr12:104381000-104387400	Weak transcription	Fetal Intestine Large	intestine
25	chr12:104381000-104387600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:104381000-104387800	Weak transcription	Primary T cells from cord blood	blood
27	chr12:104381000-104387800	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr12:104381000-104387800	Weak transcription	HUVEC	blood vessel
29	chr12:104381000-104388000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr12:104381000-104388400	Weak transcription	Spleen	Spleen
31	chr12:104381000-104389000	Weak transcription	Thymus	Thymus
32	chr12:104381000-104390600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr12:104381000-104390800	Weak transcription	K562	blood
34	chr12:104381000-104391200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr12:104381000-104391200	Weak transcription	Right Ventricle	heart
36	chr12:104381000-104400200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr12:104381600-104386400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr12:104381600-104392800	Weak transcription	Left Ventricle	heart
39	chr12:104382600-104389000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr12:104383400-104387800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr12:104383400-104388000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr12:104383400-104388200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr12:104383600-104386400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr12:104383600-104386800	Weak transcription	Adipose Nuclei	Adipose
45	chr12:104383600-104389600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr12:104383800-104386600	Weak transcription	Dnd41	blood
47	chr12:104384000-104387400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr12:104384200-104386400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:104384600-104386400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr12:104384600-104387200	Weak transcription	Primary T helper cells fromperipheralblood	blood

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