Variant report

Variant	rs2002860
Chromosome Location	chr4:8456701-8456702
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	POLR2A	chr4:8455263-8456733	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000251186	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11729265	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12503034	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1880025	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2049302	0.91[ASN][1000 genomes]
rs2140336	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2245515	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2245808	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2245809	0.92[ASN][1000 genomes]
rs2386223	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2631723	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2631724	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2631727	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2631728	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2631729	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2631730	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2631733	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2631737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2631752	0.85[ASN][1000 genomes]
rs2631757	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2631763	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2631764	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2631765	0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2631766	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2631767	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2631769	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688221	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2688228	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2688229	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2688230	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2688234	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688239	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2688240	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2688244	0.94[ASN][1000 genomes]
rs2688246	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3103090	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3103098	0.82[CEU][hapmap];0.81[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3115396	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3775893	0.84[EUR][1000 genomes]
rs4325994	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56343159	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs954270	0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.91[ASN][1000 genomes]
rs954271	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2002860	C4orf23	cis	cerebellum	SCAN
rs2002860	ACOX3	cis	parietal	SCAN
rs2002860	TBC1D14	cis	parietal	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	chr4:8444800-8458400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:8445000-8460800	Weak transcription	Psoas Muscle	Psoas
4	chr4:8445200-8461400	Weak transcription	Hela-S3	cervix
5	chr4:8446400-8457400	Strong transcription	Fetal Intestine Small	intestine
6	chr4:8446400-8463200	Strong transcription	Stomach Smooth Muscle	stomach
7	chr4:8446400-8473800	Strong transcription	Fetal Stomach	stomach
8	chr4:8446600-8463600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr4:8446600-8463600	Strong transcription	Thymus	Thymus
10	chr4:8446600-8464600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:8446600-8473400	Strong transcription	Dnd41	blood
12	chr4:8446600-8474000	Strong transcription	Fetal Muscle Leg	muscle
13	chr4:8446800-8456800	Strong transcription	Fetal Muscle Trunk	muscle
14	chr4:8446800-8463800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr4:8447000-8458200	Strong transcription	HepG2	liver
16	chr4:8447000-8461800	Strong transcription	Fetal Intestine Large	intestine
17	chr4:8447000-8464000	Strong transcription	Primary B cells from cord blood	blood
18	chr4:8447000-8474400	Strong transcription	Fetal Brain Female	brain
19	chr4:8447000-8475200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:8447000-8480200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:8447200-8457400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:8447200-8458000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:8447200-8458200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr4:8447200-8464200	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr4:8447200-8473000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr4:8447200-8480200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr4:8447400-8463600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr4:8447400-8474000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr4:8447400-8482200	Strong transcription	Primary T cells from cord blood	blood
30	chr4:8447600-8464000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr4:8447600-8472200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr4:8447600-8473400	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr4:8447800-8458400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr4:8447800-8459800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr4:8447800-8461200	Strong transcription	Liver	Liver
36	chr4:8447800-8461800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:8447800-8463400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr4:8447800-8463400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr4:8447800-8463600	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr4:8447800-8463800	Strong transcription	Brain Cingulate Gyrus	brain
41	chr4:8447800-8472800	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr4:8448000-8461400	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr4:8448000-8461600	Strong transcription	Duodenum Mucosa	Duodenum
44	chr4:8448000-8461800	Strong transcription	Primary B cells from peripheral blood	blood
45	chr4:8448000-8462000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr4:8448000-8463200	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr4:8448000-8463600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr4:8448200-8463800	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr4:8448200-8467400	Strong transcription	Adipose Nuclei	Adipose
50	chr4:8448400-8457200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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