Variant report

Variant	rs12623954
Chromosome Location	chr2:55644492-55644493
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55643936..55648492-chr2:55843198..55848689,6	K562	blood:
2	chr2:55644452..55648722-chr2:55843350..55848689,7	K562	blood:
3	chr2:55496544..55498355-chr2:55643954..55646229,2	K562	blood:

Variant related genes	Relation type
ENSG00000138041	Chromatin interaction
ENSG00000272606	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10182704	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10184756	0.93[EUR][1000 genomes]
rs10454144	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11125565	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11125566	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11125572	0.93[ASN][1000 genomes]
rs12612806	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12617891	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12618216	0.92[ASN][1000 genomes]
rs12618795	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12713297	0.86[ASN][1000 genomes]
rs13416912	0.90[EUR][1000 genomes]
rs1454415	0.98[ASN][1000 genomes]
rs1454419	1.00[ASN][1000 genomes]
rs1454420	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1454423	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1454424	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545554	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1902056	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1902057	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1902058	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1902061	0.90[ASN][1000 genomes]
rs1902062	0.82[ASN][1000 genomes]
rs2045132	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2045133	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2045134	0.96[ASN][1000 genomes]
rs2045135	0.98[ASN][1000 genomes]
rs2045136	0.91[ASN][1000 genomes]
rs2123983	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2219130	0.93[EUR][1000 genomes]
rs2576688	0.96[EUR][1000 genomes]
rs2576703	0.96[EUR][1000 genomes]
rs2589057	0.96[EUR][1000 genomes]
rs2589068	0.96[EUR][1000 genomes]
rs2589069	0.96[EUR][1000 genomes]
rs2589070	0.96[EUR][1000 genomes]
rs2589078	0.96[EUR][1000 genomes]
rs2589079	0.96[EUR][1000 genomes]
rs2589104	0.96[EUR][1000 genomes]
rs2864831	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2864832	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2867173	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2867178	0.93[EUR][1000 genomes]
rs2867179	0.93[EUR][1000 genomes]
rs2867194	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2902857	0.90[EUR][1000 genomes]
rs2903507	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2903509	0.93[EUR][1000 genomes]
rs2903514	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2917777	0.96[EUR][1000 genomes]
rs2920970	0.90[EUR][1000 genomes]
rs2966466	0.90[EUR][1000 genomes]
rs3099080	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3099081	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3099083	0.90[EUR][1000 genomes]
rs3111408	0.88[EUR][1000 genomes]
rs3111409	0.88[EUR][1000 genomes]
rs3748943	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762511	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3974263	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4233960	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4233961	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4277563	0.98[ASN][1000 genomes]
rs4481025	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4535081	0.93[EUR][1000 genomes]
rs4672030	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4672032	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4672033	0.93[EUR][1000 genomes]
rs4672036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4672037	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4672038	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4672040	0.98[ASN][1000 genomes]
rs4672041	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4672043	0.93[ASN][1000 genomes]
rs4672044	0.93[ASN][1000 genomes]
rs59634508	0.96[EUR][1000 genomes]
rs61157332	0.96[EUR][1000 genomes]
rs6545489	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6545490	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6545491	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6545492	0.98[ASN][1000 genomes]
rs6709204	0.93[EUR][1000 genomes]
rs6710192	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6718031	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6718909	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6720698	0.97[ASN][1000 genomes]
rs6721593	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6724840	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6725968	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6732633	0.89[ASN][1000 genomes]
rs6732759	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6733814	0.98[ASN][1000 genomes]
rs6744426	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6748979	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72924907	0.90[EUR][1000 genomes]
rs7424286	0.94[ASN][1000 genomes]
rs7557555	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7557956	0.89[EUR][1000 genomes]
rs7579037	0.98[ASN][1000 genomes]
rs7586440	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7601588	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7602189	0.98[ASN][1000 genomes]
rs7606361	0.82[AMR][1000 genomes];0.90[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	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers 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 target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55542400-55644800	Weak transcription	Primary T cells from cord blood	blood
2	chr2:55591000-55646000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:55601800-55644600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:55624400-55645600	Weak transcription	Ovary	ovary
5	chr2:55628600-55646000	Weak transcription	Esophagus	oesophagus
6	chr2:55630400-55645800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr2:55630800-55644800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr2:55630800-55645200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:55630800-55645200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:55631000-55645400	Weak transcription	Placenta	Placenta
11	chr2:55631800-55645200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr2:55632000-55644800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr2:55632600-55645800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:55632800-55645800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:55633000-55645000	Weak transcription	Liver	Liver
16	chr2:55633000-55645800	Weak transcription	Fetal Intestine Small	intestine
17	chr2:55633000-55645800	Weak transcription	Spleen	Spleen
18	chr2:55633000-55646000	Weak transcription	Lung	lung
19	chr2:55633200-55644800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr2:55636800-55645600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:55637400-55644600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr2:55637400-55645000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:55639800-55645600	Weak transcription	Aorta	Aorta
24	chr2:55639800-55645800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:55640000-55645600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr2:55640200-55645800	Weak transcription	Left Ventricle	heart
27	chr2:55640400-55645600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr2:55640600-55645400	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr2:55640800-55646000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:55641000-55644800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:55641000-55645600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr2:55641000-55645600	Weak transcription	Thymus	Thymus
33	chr2:55642600-55646600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:55642600-55648200	Active TSS	GM12878-XiMat	blood
35	chr2:55642800-55645800	Weak transcription	Pancreas	Pancrea
36	chr2:55643000-55645000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr2:55643000-55645600	Weak transcription	Right Ventricle	heart
38	chr2:55643000-55648000	Active TSS	Brain Germinal Matrix	brain
39	chr2:55643200-55644800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:55643200-55645000	Weak transcription	Colon Smooth Muscle	Colon
41	chr2:55643200-55647600	Active TSS	K562	blood
42	chr2:55643200-55648000	Active TSS	Fetal Brain Female	brain
43	chr2:55643200-55648200	Active TSS	Brain Cingulate Gyrus	brain
44	chr2:55643200-55648200	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr2:55643400-55644600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:55643600-55647600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:55643800-55644600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:55643800-55644800	Flanking Active TSS	Osteobl	bone
49	chr2:55643800-55645400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:55643800-55645400	Flanking Active TSS	Dnd41	blood

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