Variant report

Variant	rs4696828
Chromosome Location	chr4:8455604-8455605
allele	A/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	POLR2A	chr4:8455263-8456733	K562	blood:	n/a	n/a
2	POLR2A	chr4:8455579-8456124	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
TRMT44	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10461079	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1357481	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1543246	0.87[ASN][1000 genomes]
rs1880023	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1880024	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1916326	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1949733	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2010758	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2140337	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2386227	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2450475	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2631731	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2631734	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2631735	1.00[CEU][hapmap];0.86[GIH][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.99[EUR][1000 genomes]
rs2631736	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2631740	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2631742	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2631743	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2631744	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2631745	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2631746	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2631754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2631756	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2631758	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2631762	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2631768	0.81[CEU][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs2688219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2688223	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]
rs2688224	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2688227	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2688231	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2688233	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2688235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2688242	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2688243	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2688247	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3103067	1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3103069	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3103070	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3103071	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3103072	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3103099	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6447875	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6837429	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6845969	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6858542	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs868105	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs871768	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs940133	0.89[YRI][hapmap];0.82[EUR][1000 genomes]
rs940134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs940136	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv461220	chr4:8372944-8458394	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv593638	chr4:8372944-8458394	Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4696828	ACOX3	cis	lymphoblastoid	seeQTL
rs4696828	RP11-689P11.2	cis	lung	GTEx
rs4696828	TRMT44	cis	Nerve Tibial	GTEx
rs4696828	STK32B	cis	cerebellum	SCAN
rs4696828	TBC1D14	cis	parietal	SCAN
rs4696828	C4orf6	cis	cerebellum	SCAN
rs4696828	C4orf23	cis	parietal	SCAN
rs4696828	C4orf23	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8444200-8456800	Weak transcription	A549	lung
2	chr4:8444600-8455800	Weak transcription	NHDF-Ad	bronchial
3	chr4:8444800-8458400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr4:8445000-8460800	Weak transcription	Psoas Muscle	Psoas
5	chr4:8445200-8461400	Weak transcription	Hela-S3	cervix
6	chr4:8446400-8457400	Strong transcription	Fetal Intestine Small	intestine
7	chr4:8446400-8463200	Strong transcription	Stomach Smooth Muscle	stomach
8	chr4:8446400-8473800	Strong transcription	Fetal Stomach	stomach
9	chr4:8446600-8463600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:8446600-8463600	Strong transcription	Thymus	Thymus
11	chr4:8446600-8464600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:8446600-8473400	Strong transcription	Dnd41	blood
13	chr4:8446600-8474000	Strong transcription	Fetal Muscle Leg	muscle
14	chr4:8446800-8456800	Strong transcription	Fetal Muscle Trunk	muscle
15	chr4:8446800-8463800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr4:8447000-8458200	Strong transcription	HepG2	liver
17	chr4:8447000-8461800	Strong transcription	Fetal Intestine Large	intestine
18	chr4:8447000-8464000	Strong transcription	Primary B cells from cord blood	blood
19	chr4:8447000-8474400	Strong transcription	Fetal Brain Female	brain
20	chr4:8447000-8475200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr4:8447000-8480200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:8447200-8457400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr4:8447200-8458000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:8447200-8458200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr4:8447200-8464200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr4:8447200-8473000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr4:8447200-8480200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr4:8447400-8463600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:8447400-8474000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr4:8447400-8482200	Strong transcription	Primary T cells from cord blood	blood
31	chr4:8447600-8464000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr4:8447600-8472200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr4:8447600-8473400	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr4:8447800-8458400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:8447800-8459800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr4:8447800-8461200	Strong transcription	Liver	Liver
37	chr4:8447800-8461800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr4:8447800-8463400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr4:8447800-8463400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr4:8447800-8463600	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr4:8447800-8463800	Strong transcription	Brain Cingulate Gyrus	brain
42	chr4:8447800-8472800	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr4:8448000-8461400	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr4:8448000-8461600	Strong transcription	Duodenum Mucosa	Duodenum
45	chr4:8448000-8461800	Strong transcription	Primary B cells from peripheral blood	blood
46	chr4:8448000-8462000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:8448000-8463200	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr4:8448000-8463600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr4:8448200-8463800	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr4:8448200-8467400	Strong transcription	Adipose Nuclei	Adipose

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