Variant report

Variant	rs7600339
Chromosome Location	chr2:55557192-55557193
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55546328..55548637-chr2:55556115..55557896,2	K562	blood:
2	chr2:55509212..55512081-chr2:55556525..55559325,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162997	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10169061	0.81[AMR][1000 genomes]
rs10169395	0.82[ASN][1000 genomes]
rs10172058	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10189439	0.86[AFR][1000 genomes]
rs10191937	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1045613	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10496042	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11125564	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11678347	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11902837	0.83[AMR][1000 genomes]
rs12614357	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12617887	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12621289	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12621495	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12713293	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12713294	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12713295	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12713296	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12991401	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13001912	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13010237	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13010255	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13013113	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13019339	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13022424	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13028925	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1349884	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1349885	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1370360	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1370361	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1902060	0.83[AMR][1000 genomes]
rs1992127	0.83[AFR][1000 genomes]
rs1992128	0.83[AFR][1000 genomes]
rs2198575	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2576705	0.80[AFR][1000 genomes]
rs2576706	0.85[AFR][1000 genomes]
rs2589055	0.87[AFR][1000 genomes]
rs2589056	0.86[AFR][1000 genomes]
rs2589066	0.86[AFR][1000 genomes]
rs2867174	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2867175	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2867176	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2867177	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3791633	0.86[AFR][1000 genomes]
rs3791634	0.86[AFR][1000 genomes]
rs3791642	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3791650	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3791652	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3828235	0.82[AMR][1000 genomes]
rs6545487	0.86[AFR][1000 genomes]
rs6545488	0.83[AFR][1000 genomes]
rs66882175	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6724338	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6727038	0.85[AFR][1000 genomes]
rs6746104	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6747649	0.83[AMR][1000 genomes]
rs6752182	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6754930	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6756777	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74181227	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7558687	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7561473	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7569535	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7572492	0.82[EUR][1000 genomes]
rs7589390	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7606505	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9789365	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	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
3	nsv874157	chr2:55483020-55571085	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv874158	chr2:55513738-55619923	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	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
6	nsv457941	chr2:55517491-55585915	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv582030	chr2:55517491-55585915	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7600339	CCDC88A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55510000-55578800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:55510200-55559000	Weak transcription	Psoas Muscle	Psoas
3	chr2:55510200-55616800	Weak transcription	Fetal Intestine Small	intestine
4	chr2:55512400-55577400	Weak transcription	Right Ventricle	heart
5	chr2:55518600-55591400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:55519800-55579000	Weak transcription	Primary B cells from cord blood	blood
7	chr2:55520400-55591200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr2:55521400-55591000	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr2:55523000-55584400	Weak transcription	Aorta	Aorta
10	chr2:55523200-55584800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr2:55523600-55600600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:55534200-55589400	Weak transcription	Pancreas	Pancrea
13	chr2:55537800-55609400	Weak transcription	Lung	lung
14	chr2:55539200-55567800	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:55539200-55579000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:55539200-55579000	Weak transcription	NHEK	skin
17	chr2:55541400-55564600	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr2:55541400-55584400	Weak transcription	Spleen	Spleen
19	chr2:55541600-55557600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr2:55541800-55574800	Weak transcription	Ovary	ovary
21	chr2:55542400-55559800	Weak transcription	Fetal Brain Male	brain
22	chr2:55542400-55560400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:55542400-55589800	Weak transcription	Fetal Intestine Large	intestine
24	chr2:55542400-55644800	Weak transcription	Primary T cells from cord blood	blood
25	chr2:55542600-55563000	Weak transcription	Thymus	Thymus
26	chr2:55544200-55581800	Weak transcription	Left Ventricle	heart
27	chr2:55546200-55557200	Weak transcription	HUVEC	blood vessel
28	chr2:55546200-55585000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr2:55546600-55579000	Weak transcription	K562	blood
30	chr2:55546800-55578800	Weak transcription	GM12878-XiMat	blood
31	chr2:55547400-55590600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr2:55548200-55585000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:55548600-55560800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr2:55548600-55574800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:55548800-55570000	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr2:55548800-55574800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:55551200-55558200	Strong transcription	HSMM	muscle
38	chr2:55551800-55577000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr2:55552000-55558200	Strong transcription	Fetal Lung	lung
40	chr2:55552000-55558800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:55552200-55558800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr2:55552600-55558600	Strong transcription	Dnd41	blood
43	chr2:55552600-55567000	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr2:55552800-55558400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:55553200-55557800	Strong transcription	Fetal Muscle Leg	muscle
46	chr2:55553400-55564600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:55553400-55577200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:55553800-55557200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr2:55553800-55558400	Strong transcription	Fetal Brain Female	brain
50	chr2:55553800-55558400	Strong transcription	Fetal Muscle Trunk	muscle

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