Variant report

Variant	rs11687771
Chromosome Location	chr2:48755336-48755337
allele	A/T
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	POLR2A	chr2:48755255-48755388	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
STON1	TF binding region
STON1-GTF2A1L	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10195717	0.86[CEU][hapmap]
rs11674217	1.00[CEU][hapmap]
rs11675947	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11678934	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs11679685	0.87[AMR][1000 genomes]
rs11683202	0.82[CEU][hapmap]
rs11687461	0.86[CEU][hapmap]
rs11687498	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11689285	1.00[CEU][hapmap]
rs11689288	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11690526	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11692537	1.00[CEU][hapmap]
rs11693784	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11694955	0.82[AMR][1000 genomes]
rs13398456	0.86[CEU][hapmap]
rs17397449	0.82[CEU][hapmap]
rs2937	1.00[CEU][hapmap];0.91[AMR][1000 genomes]
rs34026270	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34542838	0.82[EUR][1000 genomes]
rs3828341	1.00[JPT][hapmap]
rs4364065	0.87[AMR][1000 genomes]
rs7570877	0.85[EUR][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	nsv1005954	chr2:48692696-48905723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv535682	chr2:48692696-48905723	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv833981	chr2:48705444-48878179	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1007491	chr2:48752185-48796441	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv535683	chr2:48752185-48796441	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11687771	CCDC128	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48726400-48756800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:48728200-48756800	Weak transcription	HMEC	breast
3	chr2:48737800-48756200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:48738000-48755400	Weak transcription	HUVEC	blood vessel
5	chr2:48738000-48756800	Weak transcription	NH-A	brain
6	chr2:48740000-48756000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:48740000-48757600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:48742400-48756200	Weak transcription	NHDF-Ad	bronchial
9	chr2:48743200-48756000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr2:48743200-48756200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:48743200-48756800	Weak transcription	Stomach Mucosa	stomach
12	chr2:48743400-48756200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr2:48743400-48756400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr2:48743400-48757400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:48743400-48757400	Weak transcription	Gastric	stomach
16	chr2:48744000-48756600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:48744000-48756800	Weak transcription	Colonic Mucosa	Colon
18	chr2:48744600-48756400	Weak transcription	Brain Germinal Matrix	brain
19	chr2:48744800-48755800	Weak transcription	HepG2	liver
20	chr2:48744800-48756200	Weak transcription	Fetal Brain Female	brain
21	chr2:48745200-48756200	Weak transcription	Esophagus	oesophagus
22	chr2:48745600-48756800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr2:48745800-48756400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr2:48745800-48756400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:48745800-48756400	Weak transcription	Brain Angular Gyrus	brain
26	chr2:48745800-48756400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:48746000-48756400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:48746000-48756400	Weak transcription	A549	lung
29	chr2:48746000-48756400	Weak transcription	HSMM	muscle
30	chr2:48746400-48756400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr2:48746800-48756600	Weak transcription	Osteobl	bone
32	chr2:48746800-48756800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:48747000-48756000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr2:48747000-48756800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:48747000-48756800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:48748200-48756400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr2:48748200-48756400	Weak transcription	GM12878-XiMat	blood
38	chr2:48748200-48756800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:48748200-48756800	Weak transcription	NHEK	skin
40	chr2:48748400-48756000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr2:48748600-48756200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr2:48748600-48756400	Weak transcription	Dnd41	blood
43	chr2:48748800-48756400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr2:48749400-48755400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:48749400-48755800	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr2:48749400-48756200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr2:48749400-48756400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:48749400-48756400	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr2:48749400-48756400	Weak transcription	Fetal Thymus	thymus
50	chr2:48749400-48756400	Weak transcription	Thymus	Thymus

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