Variant report

Variant	rs3762511
Chromosome Location	chr2:55648131-55648132
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr2:55646315-55648449	GM12878	blood:	n/a	chr2:55647260-55647276
2	JUN	chr2:55645058-55648415	K562	blood:	n/a	chr2:55647729-55647736 chr2:55647728-55647739 chr2:55645468-55645477 chr2:55647729-55647737 chr2:55647729-55647737
3	MXI1	chr2:55644654-55648547	SK-N-SH	brain:	n/a	n/a
4	MXI1	chr2:55648111-55648425	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55643936..55648492-chr2:55843198..55848689,6	K562	blood:
2	chr2:55458950..55461087-chr2:55647562..55649544,2	K562	blood:
3	chr2:55644452..55648722-chr2:55843350..55848689,7	K562	blood:
4	chr2:55645285..55648583-chr2:55745099..55748276,4	K562	blood:
5	chr2:55508669..55511212-chr2:55645960..55648569,3	MCF-7	breast:
6	chr2:55645285..55648583-chr2:55744780..55749543,7	K562	blood:
7	chr2:55508571..55512777-chr2:55645734..55648780,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC104-5	chr2:55646412-55648361	NONHSAT070787

Variant related genes	Relation type
CCDC88A	TF binding region
ENSG00000272606	Chromatin interaction
ENSG00000143947	Chromatin interaction
ENSG00000163001	Chromatin interaction
ENSG00000162994	Chromatin interaction
ENSG00000162997	Chromatin interaction
ENSG00000138041	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10182704	0.90[EUR][1000 genomes]
rs10184756	0.93[EUR][1000 genomes]
rs10454144	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11125565	0.90[EUR][1000 genomes]
rs11125566	0.90[EUR][1000 genomes]
rs11125572	0.93[ASN][1000 genomes]
rs12612806	0.93[EUR][1000 genomes]
rs12617891	0.90[EUR][1000 genomes]
rs12618216	0.92[ASN][1000 genomes]
rs12618795	0.93[EUR][1000 genomes]
rs12623954	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713297	0.86[ASN][1000 genomes]
rs13416912	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1454415	0.98[ASN][1000 genomes]
rs1454419	1.00[ASN][1000 genomes]
rs1454420	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1454423	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1454424	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545554	0.90[EUR][1000 genomes]
rs1902056	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1902057	0.93[EUR][1000 genomes]
rs1902058	0.93[EUR][1000 genomes]
rs1902061	0.90[ASN][1000 genomes]
rs1902062	0.82[ASN][1000 genomes]
rs2045132	0.93[EUR][1000 genomes]
rs2045133	1.00[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	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2219130	0.93[EUR][1000 genomes]
rs2576688	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2576703	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2589057	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2589068	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2589069	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2589070	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2589078	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2589079	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2589104	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2864831	0.90[EUR][1000 genomes]
rs2864832	0.90[EUR][1000 genomes]
rs2867173	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2867178	0.93[EUR][1000 genomes]
rs2867179	0.93[EUR][1000 genomes]
rs2867194	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2902857	0.90[EUR][1000 genomes]
rs2903507	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2903509	0.93[EUR][1000 genomes]
rs2903514	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2917777	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2920970	0.90[EUR][1000 genomes]
rs2966466	0.90[EUR][1000 genomes]
rs3099080	0.90[EUR][1000 genomes]
rs3099081	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3099083	0.90[EUR][1000 genomes]
rs3111408	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3111409	0.88[EUR][1000 genomes]
rs3748943	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3974263	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4233960	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4233961	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4277563	0.98[ASN][1000 genomes]
rs4481025	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4535081	0.93[EUR][1000 genomes]
rs4672030	0.81[EUR][1000 genomes]
rs4672032	0.93[EUR][1000 genomes]
rs4672033	0.93[EUR][1000 genomes]
rs4672036	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4672037	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4672038	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4672040	0.98[ASN][1000 genomes]
rs4672041	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4672043	0.93[ASN][1000 genomes]
rs4672044	0.93[ASN][1000 genomes]
rs59634508	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61157332	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6545489	0.93[EUR][1000 genomes]
rs6545490	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6545491	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6545492	0.98[ASN][1000 genomes]
rs6709204	0.93[EUR][1000 genomes]
rs6710192	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6718031	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6718909	0.90[EUR][1000 genomes]
rs6720698	0.97[ASN][1000 genomes]
rs6721593	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6724840	0.93[EUR][1000 genomes]
rs6725968	0.90[EUR][1000 genomes]
rs6732633	0.89[ASN][1000 genomes]
rs6732759	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6733814	0.98[ASN][1000 genomes]
rs6744426	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6748979	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72924907	0.90[EUR][1000 genomes]
rs7424286	0.94[ASN][1000 genomes]
rs7557555	0.88[EUR][1000 genomes]
rs7557956	0.89[EUR][1000 genomes]
rs7579037	0.98[ASN][1000 genomes]
rs7586440	0.86[EUR][1000 genomes]
rs7595396	0.82[AMR][1000 genomes]
rs7601588	0.87[EUR][1000 genomes]
rs7602189	0.98[ASN][1000 genomes]
rs7606361	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:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55642600-55648200	Active TSS	GM12878-XiMat	blood
2	chr2:55643200-55648200	Active TSS	Brain Cingulate Gyrus	brain
3	chr2:55643200-55648200	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr2:55643800-55648400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:55643800-55648400	Active TSS	NHLF	lung
6	chr2:55644000-55648400	Active TSS	Brain Anterior Caudate	brain
7	chr2:55644200-55648200	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr2:55644200-55648400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:55644400-55648200	Active TSS	Muscle Satellite Cultured Cells	--
10	chr2:55644600-55648200	Active TSS	A549	lung
11	chr2:55645600-55648200	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr2:55645600-55648200	Active TSS	Thymus	Thymus
13	chr2:55646400-55648200	Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr2:55647200-55648200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr2:55647400-55648200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:55647400-55648400	Flanking Active TSS	Primary T cells from cord blood	blood
17	chr2:55647400-55648400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr2:55647400-55648800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:55647600-55648200	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr2:55647600-55648400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr2:55647600-55648800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:55647800-55648200	Flanking Active TSS	Fetal Lung	lung
23	chr2:55647800-55648200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
24	chr2:55647800-55648200	Enhancers	Small Intestine	intestine
25	chr2:55647800-55648400	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr2:55647800-55648400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:55647800-55648800	Enhancers	Fetal Brain Male	brain
28	chr2:55647800-55652400	Weak transcription	Stomach Mucosa	stomach
29	chr2:55648000-55648200	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr2:55648000-55648200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:55648000-55648200	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr2:55648000-55648200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr2:55648000-55648200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:55648000-55648200	Enhancers	Duodenum Mucosa	Duodenum
35	chr2:55648000-55648200	Active TSS	HepG2	liver
36	chr2:55648000-55648200	Enhancers	Osteobl	bone
37	chr2:55648000-55648400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:55648000-55648400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr2:55648000-55648400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:55648000-55648400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr2:55648000-55648400	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr2:55648000-55648400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:55648000-55648400	Enhancers	Brain Substantia Nigra	brain
44	chr2:55648000-55648400	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr2:55648000-55648400	Enhancers	Fetal Kidney	kidney
46	chr2:55648000-55648400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr2:55648000-55648400	Enhancers	Dnd41	blood
48	chr2:55648000-55648400	Enhancers	Hela-S3	cervix
49	chr2:55648000-55648600	Enhancers	Primary T cells fromperipheralblood	blood
50	chr2:55648000-55648600	Enhancers	Primary T helper naive cells from peripheral blood	blood

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