Variant report

Variant	rs34461314
Chromosome Location	chr2:48756682-48756683
allele	C/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	ZNF263	chr2:48756209-48758874	HEK293-T-REx	kidney:	n/a	n/a
2	MAZ	chr2:48756460-48757862	K562	blood:	n/a	chr2:48756809-48756819
3	MAZ	chr2:48756430-48759198	IMR90	lung:	n/a	chr2:48756809-48756819
4	POLR2A	chr2:48756458-48756723	H1-hESC	embryonic stem cell:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STON1-1	chr2:48756522-48756726	NONHSAT070625

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

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10184783	0.90[ASN][1000 genomes]
rs10209255	0.82[EUR][1000 genomes]
rs11125173	0.82[EUR][1000 genomes]
rs12616834	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12618125	0.95[EUR][1000 genomes]
rs12620002	0.84[ASN][1000 genomes]
rs13410391	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2177487	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2177488	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4073573	0.81[EUR][1000 genomes]
rs4131784	0.83[EUR][1000 genomes]
rs4296472	0.82[ASN][1000 genomes]
rs4528813	0.97[EUR][1000 genomes]
rs4641991	0.97[EUR][1000 genomes]
rs4952914	0.87[EUR][1000 genomes]
rs4953587	0.97[EUR][1000 genomes]
rs59356309	0.83[EUR][1000 genomes]
rs6545047	0.99[EUR][1000 genomes]
rs6733533	0.97[ASN][1000 genomes]
rs6754946	0.99[EUR][1000 genomes]
rs72822226	0.82[EUR][1000 genomes]
rs72822230	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
6	esv3390375	chr2:48755948-48758496	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3359548	chr2:48756073-48758621	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs34461314	CCDC128	Cis_1M	lymphoblastoid	RTeQTL
rs34461314	PPP1R21	cis	Thyroid	GTEx

Chromatin state (count:121 , 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	chr2:48738000-48756800	Weak transcription	NH-A	brain
4	chr2:48740000-48757600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:48743200-48756800	Weak transcription	Stomach Mucosa	stomach
6	chr2:48743400-48757400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:48743400-48757400	Weak transcription	Gastric	stomach
8	chr2:48744000-48756800	Weak transcription	Colonic Mucosa	Colon
9	chr2:48745600-48756800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr2:48746800-48756800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:48747000-48756800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:48747000-48756800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:48748200-48756800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:48748200-48756800	Weak transcription	NHEK	skin
15	chr2:48749600-48756800	Weak transcription	Liver	Liver
16	chr2:48750200-48756800	Weak transcription	Primary T cells from cord blood	blood
17	chr2:48752800-48756800	Enhancers	Fetal Stomach	stomach
18	chr2:48753200-48757000	Weak transcription	Primary B cells from cord blood	blood
19	chr2:48754800-48756800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:48754800-48756800	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr2:48754800-48756800	Enhancers	Fetal Muscle Leg	muscle
22	chr2:48754800-48756800	Enhancers	Placenta	Placenta
23	chr2:48755200-48756800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:48755200-48756800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:48755200-48756800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:48755200-48756800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr2:48755200-48756800	Weak transcription	HSMMtube	muscle
28	chr2:48755400-48756800	Enhancers	HUVEC	blood vessel
29	chr2:48755600-48756800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:48755800-48756800	Enhancers	Adipose Nuclei	Adipose
31	chr2:48755800-48756800	Enhancers	Right Ventricle	heart
32	chr2:48756000-48756800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr2:48756000-48756800	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr2:48756000-48756800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr2:48756000-48756800	Weak transcription	Brain Hippocampus Middle	brain
36	chr2:48756000-48756800	Enhancers	Left Ventricle	heart
37	chr2:48756200-48756800	Enhancers	H1 Cell Line	embryonic stem cell
38	chr2:48756200-48756800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr2:48756200-48756800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr2:48756200-48756800	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr2:48756200-48756800	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr2:48756200-48756800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
43	chr2:48756200-48756800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
44	chr2:48756200-48756800	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr2:48756200-48756800	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr2:48756200-48756800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr2:48756200-48756800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr2:48756200-48756800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:48756200-48756800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:48756200-48756800	Enhancers	Esophagus	oesophagus

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