Variant report

Variant	rs2688223
Chromosome Location	chr4:8471398-8471399
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:8471068-8471563	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:8471236-8471870	GM12891	blood:	n/a	n/a
3	POLR2A	chr4:8471024-8471970	GM12892	blood:	n/a	n/a
4	POLR2A	chr4:8471062-8472237	GM12892	blood:	n/a	n/a
5	POLR2A	chr4:8470406-8476371	K562	blood:	n/a	n/a
6	POLR2A	chr4:8471228-8471648	GM12878	blood:	n/a	n/a
7	POLR2A	chr4:8470888-8471644	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:8451706..8454826-chr4:8468396..8471846,3	K562	blood:
2	chr4:8470272..8471640-chr4:8595955..8596822,5	MCF-7	breast:
3	chr4:8470834..8472351-chr4:8587366..8589099,2	MCF-7	breast:
4	chr4:8470225..8471528-chr4:8595848..8597093,11	K562	blood:
5	chr4:8469952..8472230-chr4:8539162..8541122,2	MCF-7	breast:
6	chr4:8470159..8471594-chr4:8587070..8589399,12	MCF-7	breast:
7	chr4:8471024..8473735-chr4:8474244..8476611,2	K562	blood:

No data

Variant related genes	Relation type
TRMT44	TF binding region
ENSG00000155275	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10461079	0.91[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes]
rs1357481	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1543246	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1880023	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1880024	0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1916326	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1949733	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2010758	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2140337	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2255501	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2386227	0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2450475	0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2631731	0.95[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2631734	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2631735	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2631736	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2631740	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2631742	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2631743	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2631744	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2631745	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2631746	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2631754	0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2631756	0.90[AMR][1000 genomes]
rs2631758	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2631762	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2688219	0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2688224	0.81[AMR][1000 genomes]
rs2688227	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2688231	0.94[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2688233	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2688235	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2688242	0.94[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2688243	0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2688247	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3103067	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3103069	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3103070	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3103071	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3103072	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3103099	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4696828	0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6447875	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6837429	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6845969	0.83[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs6858542	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs868105	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs871768	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs940133	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs940134	0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs940136	0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[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	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv829854	chr4:8402921-8506407	Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv964737	chr4:8467874-8473530	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2688223	TRMT44	cis	Nerve Tibial	GTEx
rs2688223	ACOX3	Cis_1M	lymphoblastoid	RTeQTL
rs2688223	RP11-689P11.2	cis	lung	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8446400-8473800	Strong transcription	Fetal Stomach	stomach
2	chr4:8446600-8473400	Strong transcription	Dnd41	blood
3	chr4:8446600-8474000	Strong transcription	Fetal Muscle Leg	muscle
4	chr4:8447000-8474400	Strong transcription	Fetal Brain Female	brain
5	chr4:8447000-8475200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:8447000-8480200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:8447200-8473000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr4:8447200-8480200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr4:8447400-8474000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr4:8447400-8482200	Strong transcription	Primary T cells from cord blood	blood
11	chr4:8447600-8472200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr4:8447600-8473400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr4:8447800-8472800	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr4:8451200-8473600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:8458200-8472000	Weak transcription	Fetal Heart	heart
16	chr4:8459400-8474000	Strong transcription	Fetal Intestine Small	intestine
17	chr4:8459800-8478800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr4:8462400-8472800	Strong transcription	Liver	Liver
19	chr4:8463000-8471600	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr4:8463400-8473800	Weak transcription	Fetal Kidney	kidney
21	chr4:8463800-8478800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr4:8464600-8473200	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr4:8464600-8474000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr4:8464800-8472000	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr4:8464800-8472000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr4:8464800-8473400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr4:8464800-8473600	Strong transcription	Brain Angular Gyrus	brain
28	chr4:8465000-8471400	Strong transcription	Left Ventricle	heart
29	chr4:8465200-8471400	Strong transcription	Primary B cells from peripheral blood	blood
30	chr4:8465200-8471600	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr4:8465200-8471800	Strong transcription	Duodenum Mucosa	Duodenum
32	chr4:8465200-8472200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:8465200-8472200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr4:8465200-8472200	Strong transcription	Brain Cingulate Gyrus	brain
35	chr4:8465200-8472200	Strong transcription	Brain Hippocampus Middle	brain
36	chr4:8465200-8472200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr4:8465200-8472200	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr4:8465200-8472200	Strong transcription	Osteobl	bone
39	chr4:8465200-8472800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr4:8465200-8472800	Strong transcription	Aorta	Aorta
41	chr4:8465200-8473600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:8465200-8474000	Strong transcription	Lung	lung
43	chr4:8465200-8482200	Strong transcription	Brain Germinal Matrix	brain
44	chr4:8465400-8471800	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr4:8465400-8472000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:8465400-8472000	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr4:8465400-8473000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr4:8465400-8473400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr4:8465400-8473400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr4:8465400-8473400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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