Variant report

Variant	rs3762512
Chromosome Location	chr2:55648338-55648339
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	USF2	chr2:55648210-55648347	GM12878	blood:	n/a	n/a
4	MXI1	chr2:55644654-55648547	SK-N-SH	brain:	n/a	n/a
5	RFX5	chr2:55648242-55648350	GM12878	blood:	n/a	n/a
6	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
ENSG00000163001	Chromatin interaction
ENSG00000162997	Chromatin interaction
ENSG00000272606	Chromatin interaction
ENSG00000162994	Chromatin interaction
ENSG00000143947	Chromatin interaction
ENSG00000138041	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10865285	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11125567	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11680143	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11692239	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12470528	0.86[EUR][1000 genomes]
rs12471421	0.83[AMR][1000 genomes]
rs12476508	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12476548	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12713292	0.81[EUR][1000 genomes]
rs1454421	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545555	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1902059	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1982484	0.83[EUR][1000 genomes]
rs1982485	0.81[EUR][1000 genomes]
rs2198577	0.84[AMR][1000 genomes]
rs2576713	0.85[EUR][1000 genomes]
rs2576714	0.85[EUR][1000 genomes]
rs2576715	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2589073	0.85[EUR][1000 genomes]
rs2589075	0.86[EUR][1000 genomes]
rs2589077	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2589102	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2589103	0.80[EUR][1000 genomes]
rs2864829	0.81[EUR][1000 genomes]
rs2864830	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2867180	0.86[EUR][1000 genomes]
rs2867181	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2903508	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2917778	0.85[EUR][1000 genomes]
rs2920964	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3099075	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3099076	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3099077	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3099079	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3099082	0.83[AFR][1000 genomes]
rs3099084	0.83[AFR][1000 genomes]
rs3111404	0.87[EUR][1000 genomes]
rs3111410	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3111411	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3111412	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs3111413	0.87[EUR][1000 genomes]
rs35963448	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3762510	0.85[EUR][1000 genomes]
rs3791653	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4349381	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4672039	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55711116	0.86[EUR][1000 genomes]
rs55828034	0.82[EUR][1000 genomes]
rs55908714	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56133422	0.81[EUR][1000 genomes]
rs57410428	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61379198	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62137154	0.86[EUR][1000 genomes]
rs62137157	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6545493	0.83[AMR][1000 genomes]
rs6706178	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6718236	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6725124	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7425220	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7561210	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7564292	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7570934	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7575929	0.81[EUR][1000 genomes]
rs7582580	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7586529	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3762512	CCDC88A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55643800-55648400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr2:55643800-55648400	Active TSS	NHLF	lung
3	chr2:55644000-55648400	Active TSS	Brain Anterior Caudate	brain
4	chr2:55644200-55648400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:55647400-55648400	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr2:55647400-55648400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr2:55647400-55648800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:55647600-55648400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr2:55647600-55648800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:55647800-55648400	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr2:55647800-55648400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
12	chr2:55647800-55648800	Enhancers	Fetal Brain Male	brain
13	chr2:55647800-55652400	Weak transcription	Stomach Mucosa	stomach
14	chr2:55648000-55648400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:55648000-55648400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:55648000-55648400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:55648000-55648400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr2:55648000-55648400	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr2:55648000-55648400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:55648000-55648400	Enhancers	Brain Substantia Nigra	brain
21	chr2:55648000-55648400	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr2:55648000-55648400	Enhancers	Fetal Kidney	kidney
23	chr2:55648000-55648400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr2:55648000-55648400	Enhancers	Dnd41	blood
25	chr2:55648000-55648400	Enhancers	Hela-S3	cervix
26	chr2:55648000-55648600	Enhancers	Primary T cells fromperipheralblood	blood
27	chr2:55648000-55648600	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr2:55648000-55648600	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr2:55648000-55648600	Enhancers	Brain Angular Gyrus	brain
30	chr2:55648000-55648600	Enhancers	Brain Hippocampus Middle	brain
31	chr2:55648000-55648600	Enhancers	K562	blood
32	chr2:55648000-55648800	Enhancers	Primary B cells from peripheral blood	blood
33	chr2:55648000-55648800	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr2:55648000-55648800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:55648000-55649000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:55648000-55649200	Weak transcription	Fetal Heart	heart
37	chr2:55648000-55649200	Enhancers	Fetal Muscle Leg	muscle
38	chr2:55648000-55649200	Enhancers	Fetal Thymus	thymus
39	chr2:55648000-55649400	Enhancers	NHDF-Ad	bronchial
40	chr2:55648000-55649800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:55648000-55649800	Weak transcription	Colon Smooth Muscle	Colon
42	chr2:55648000-55650000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr2:55648000-55650000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:55648000-55650000	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr2:55648000-55650000	Enhancers	Brain Germinal Matrix	brain
46	chr2:55648000-55651000	Weak transcription	HMEC	breast
47	chr2:55648000-55651200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr2:55648000-55651600	Weak transcription	NHEK	skin
49	chr2:55648000-55652200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr2:55648000-55652200	Weak transcription	HUVEC	blood vessel

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