Variant report

Variant	rs55828034
Chromosome Location	chr2:55631967-55631968
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55624788..55628704-chr2:55629085..55632054,3	K562	blood:
2	chr2:55629328..55632200-chr2:55634808..55637417,2	K562	blood:
3	chr2:55629189..55632200-chr2:55632234..55637417,4	K562	blood:

Variant related genes	Relation type
ENSG00000115355	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10189439	0.84[ASN][1000 genomes]
rs10865285	0.84[ASN][1000 genomes]
rs11125567	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11680143	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11692239	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12471421	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12476508	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12476548	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12713292	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1344881	0.83[ASN][1000 genomes]
rs1437394	0.83[ASN][1000 genomes]
rs1454421	0.80[EUR][1000 genomes]
rs1545555	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1902059	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1982484	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1982485	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1992127	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1992128	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2198577	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2576687	0.83[ASN][1000 genomes]
rs2576704	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2576705	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2576706	0.84[ASN][1000 genomes]
rs2576713	0.83[ASN][1000 genomes]
rs2576714	0.83[ASN][1000 genomes]
rs2576715	0.83[ASN][1000 genomes]
rs2576716	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2576717	0.83[ASN][1000 genomes]
rs2589055	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2589056	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2589059	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2589065	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2589066	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2589072	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2589073	0.83[ASN][1000 genomes]
rs2589075	0.83[ASN][1000 genomes]
rs2589085	0.83[ASN][1000 genomes]
rs2589087	0.83[ASN][1000 genomes]
rs2589088	0.83[ASN][1000 genomes]
rs2589090	0.83[ASN][1000 genomes]
rs2589091	0.83[ASN][1000 genomes]
rs2589102	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2589103	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2589105	0.83[ASN][1000 genomes]
rs2589106	0.83[ASN][1000 genomes]
rs2864828	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2864829	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2864830	0.83[ASN][1000 genomes]
rs2867180	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2867181	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2903508	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2917776	0.87[ASN][1000 genomes]
rs2917778	0.83[ASN][1000 genomes]
rs2920971	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2920974	0.86[ASN][1000 genomes]
rs2966467	0.83[ASN][1000 genomes]
rs3099075	0.82[ASN][1000 genomes]
rs3099077	0.83[ASN][1000 genomes]
rs3099079	0.83[ASN][1000 genomes]
rs3099082	0.83[ASN][1000 genomes]
rs3099084	0.83[ASN][1000 genomes]
rs3111404	0.83[ASN][1000 genomes]
rs3111410	0.84[ASN][1000 genomes]
rs3111411	0.84[ASN][1000 genomes]
rs3111412	0.83[ASN][1000 genomes]
rs3111413	0.83[ASN][1000 genomes]
rs35963448	0.88[ASN][1000 genomes]
rs3762510	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3762512	0.82[EUR][1000 genomes]
rs3791633	0.87[ASN][1000 genomes]
rs3791634	0.87[ASN][1000 genomes]
rs3791653	0.84[ASN][1000 genomes]
rs4349381	0.88[ASN][1000 genomes]
rs4672039	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55711116	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55908714	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56133422	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56320407	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57410428	0.84[ASN][1000 genomes]
rs61379198	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62137151	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62137154	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62137157	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62138071	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6545487	0.87[ASN][1000 genomes]
rs6545488	0.87[ASN][1000 genomes]
rs6545493	0.83[ASN][1000 genomes]
rs6706178	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6718236	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6725124	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6727038	0.83[ASN][1000 genomes]
rs7425220	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7561210	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7564292	0.87[ASN][1000 genomes]
rs7570934	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7575929	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7576695	0.86[ASN][1000 genomes]
rs7582580	0.83[ASN][1000 genomes]
rs7586529	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv874159	chr2:55513738-55636351	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	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
4	esv275364	chr2:55621732-55632233	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	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
rs55828034	CCDC88A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55542400-55644800	Weak transcription	Primary T cells from cord blood	blood
2	chr2:55555200-55635800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:55579200-55640800	Weak transcription	Fetal Brain Male	brain
4	chr2:55579400-55644400	Weak transcription	Primary B cells from cord blood	blood
5	chr2:55579600-55632200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:55582000-55632400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:55589400-55639400	Weak transcription	Aorta	Aorta
8	chr2:55589600-55632200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr2:55591000-55646000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr2:55592000-55635400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:55592800-55635600	Weak transcription	HSMMtube	muscle
12	chr2:55593200-55632600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:55601800-55644600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:55612800-55632000	Weak transcription	Fetal Stomach	stomach
15	chr2:55614200-55632000	Weak transcription	Thymus	Thymus
16	chr2:55616600-55635400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr2:55616600-55635400	Weak transcription	HMEC	breast
18	chr2:55616800-55632200	Weak transcription	Hela-S3	cervix
19	chr2:55616800-55642600	Weak transcription	HUVEC	blood vessel
20	chr2:55618200-55635200	Weak transcription	Psoas Muscle	Psoas
21	chr2:55618200-55639400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr2:55618200-55642400	Weak transcription	Fetal Lung	lung
23	chr2:55618600-55636000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr2:55619000-55632200	Weak transcription	Fetal Muscle Leg	muscle
25	chr2:55619200-55636800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr2:55619600-55632000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr2:55623000-55635600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr2:55623200-55644400	Weak transcription	Fetal Kidney	kidney
29	chr2:55623600-55632200	Weak transcription	GM12878-XiMat	blood
30	chr2:55624200-55635600	Weak transcription	NHEK	skin
31	chr2:55624400-55645600	Weak transcription	Ovary	ovary
32	chr2:55624600-55632600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:55627800-55636000	Weak transcription	NHDF-Ad	bronchial
34	chr2:55628000-55632200	Weak transcription	NHLF	lung
35	chr2:55628200-55633000	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr2:55628400-55632200	Weak transcription	Left Ventricle	heart
37	chr2:55628600-55632600	Weak transcription	Fetal Intestine Small	intestine
38	chr2:55628600-55646000	Weak transcription	Esophagus	oesophagus
39	chr2:55629000-55634400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:55629000-55635600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr2:55629200-55632200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr2:55629400-55632000	Weak transcription	Liver	Liver
43	chr2:55629400-55633000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:55629400-55633800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:55629400-55634400	Strong transcription	Fetal Thymus	thymus
46	chr2:55629600-55633000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr2:55629600-55633800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:55629600-55633800	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr2:55629600-55634200	Strong transcription	Dnd41	blood
50	chr2:55629600-55636200	Weak transcription	H9 Cell Line	embryonic stem cell

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