Variant report

Variant	rs1047948
Chromosome Location	chr2:55517491-55517492
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55516323..55518543-chr2:55519705..55522425,2	MCF-7	breast:
2	chr2:55495242..55497992-chr2:55516142..55518443,2	K562	blood:
3	chr2:55512725..55515035-chr2:55515151..55518093,2	MCF-7	breast:
4	chr2:55513717..55517670-chr2:55518024..55521740,6	K562	blood:
5	chr2:55494684..55499569-chr2:55516943..55523168,5	K562	blood:
6	chr2:55516061..55518491-chr2:55518529..55520349,2	K562	blood:

Variant related genes	Relation type
ENSG00000085760	Chromatin interaction
ENSG00000206964	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11125567	0.81[CEU][hapmap];0.82[MEX][hapmap]
rs11692239	0.81[CEU][hapmap]
rs12476548	0.81[CEU][hapmap];0.86[MEX][hapmap]
rs12713292	0.80[AMR][1000 genomes]
rs1992127	0.81[CEU][hapmap]
rs1992128	0.81[CEU][hapmap]
rs2576704	0.81[CEU][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes]
rs2576705	0.81[CEU][hapmap]
rs2576716	0.80[AMR][1000 genomes]
rs2589055	0.81[CEU][hapmap]
rs2589059	0.81[CEU][hapmap];0.86[AMR][1000 genomes]
rs2589065	0.81[CEU][hapmap];0.83[AMR][1000 genomes]
rs2589066	0.80[CEU][hapmap]
rs2589072	0.81[CEU][hapmap];0.82[MEX][hapmap];0.86[AMR][1000 genomes]
rs2589090	0.87[MEX][hapmap]
rs2589102	0.81[CEU][hapmap]
rs2864829	0.81[CEU][hapmap];0.80[AMR][1000 genomes]
rs2917776	0.92[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2920971	0.81[CEU][hapmap]
rs2920974	0.88[CEU][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3762510	0.81[CEU][hapmap];0.80[AMR][1000 genomes]
rs3791633	0.92[CEU][hapmap]
rs3791634	0.92[CEU][hapmap]
rs62137154	0.80[AMR][1000 genomes]
rs66507139	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6727038	0.88[CEU][hapmap]
rs7576695	0.81[AMR][1000 genomes]
rs7603216	0.88[CEU][hapmap]

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	esv1799450	chr2:55494904-55520842	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1047948	CCDC88A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55509000-55541200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55509400-55545200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:55509600-55522600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:55509800-55518600	Weak transcription	HMEC	breast
5	chr2:55509800-55521800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:55510000-55518800	Weak transcription	Brain Angular Gyrus	brain
7	chr2:55510000-55521600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:55510000-55521600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:55510000-55521800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:55510000-55521800	Weak transcription	Fetal Brain Male	brain
11	chr2:55510000-55521800	Weak transcription	NHEK	skin
12	chr2:55510000-55522000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:55510000-55522200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:55510000-55522200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:55510000-55522400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:55510000-55522400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:55510000-55522600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr2:55510000-55541600	Weak transcription	Esophagus	oesophagus
19	chr2:55510000-55553600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:55510000-55578800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:55510200-55519200	Weak transcription	Ovary	ovary
22	chr2:55510200-55520600	Weak transcription	HSMMtube	muscle
23	chr2:55510200-55521800	Weak transcription	Fetal Kidney	kidney
24	chr2:55510200-55522200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:55510200-55522400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:55510200-55522400	Weak transcription	NHLF	lung
27	chr2:55510200-55522600	Weak transcription	Aorta	Aorta
28	chr2:55510200-55542200	Weak transcription	Fetal Intestine Large	intestine
29	chr2:55510200-55559000	Weak transcription	Psoas Muscle	Psoas
30	chr2:55510200-55616800	Weak transcription	Fetal Intestine Small	intestine
31	chr2:55510400-55522400	Weak transcription	Left Ventricle	heart
32	chr2:55510400-55529000	Weak transcription	Placenta	Placenta
33	chr2:55510600-55519400	Weak transcription	Primary B cells from cord blood	blood
34	chr2:55510600-55521800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:55510600-55522400	Weak transcription	A549	lung
36	chr2:55510600-55533800	Weak transcription	Pancreas	Pancrea
37	chr2:55510600-55536600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr2:55510600-55537400	Weak transcription	Lung	lung
39	chr2:55510800-55518200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:55510800-55518600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr2:55510800-55521200	Weak transcription	Osteobl	bone
42	chr2:55510800-55521800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr2:55510800-55542200	Weak transcription	Rectal Smooth Muscle	rectum
44	chr2:55511000-55518800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr2:55511000-55519600	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr2:55511000-55521600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:55511000-55521800	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr2:55511000-55521800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr2:55511000-55540600	Weak transcription	Spleen	Spleen
50	chr2:55511200-55519400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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