Variant report

Variant	rs2688221
Chromosome Location	chr4:8479448-8479449
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	chr4:8478856-8480731	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr4:8479274-8479460	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr4:8478899-8482832	K562	blood:	n/a	n/a
4	POLR2A	chr4:8479181-8480551	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:8473752..8477708-chr4:8479447..8482230,3	K562	blood:
2	chr4:8479058..8480948-chr4:8481115..8485111,3	MCF-7	breast:
3	chr4:8478212..8480998-chr4:8552903..8554781,2	K562	blood:

Variant related genes	Relation type
ENSG00000205959	TF binding region
ENSG00000155275	Chromatin interaction
ENSG00000205959	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11729265	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12503034	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1880025	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2002860	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]
rs2049302	0.88[ASN][1000 genomes]
rs2140336	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2245515	0.92[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2245808	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2245809	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2386223	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2631723	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2631724	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2631727	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2631728	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2631729	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2631730	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2631733	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2631737	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2631752	0.82[ASN][1000 genomes]
rs2631757	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2631763	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2631764	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2631765	0.90[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2631766	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2631767	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2631769	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2688228	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2688229	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2688230	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2688234	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2688239	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2688240	0.96[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2688244	0.91[ASN][1000 genomes]
rs2688246	0.93[ASN][1000 genomes]
rs3103090	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3103098	0.81[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs3115396	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3775893	0.84[EUR][1000 genomes]
rs4325994	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56343159	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs954270	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs954271	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8447000-8480200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr4:8447200-8480200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr4:8447400-8482200	Strong transcription	Primary T cells from cord blood	blood
4	chr4:8465200-8482200	Strong transcription	Brain Germinal Matrix	brain
5	chr4:8465400-8480200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:8467600-8482200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr4:8467800-8480400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr4:8468400-8479600	Weak transcription	Psoas Muscle	Psoas
9	chr4:8471200-8480600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr4:8471400-8479600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:8471400-8480200	Weak transcription	HMEC	breast
12	chr4:8471800-8479600	Weak transcription	NHEK	skin
13	chr4:8471800-8480000	Weak transcription	GM12878-XiMat	blood
14	chr4:8471800-8480800	Weak transcription	HepG2	liver
15	chr4:8471800-8483200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr4:8472000-8480200	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr4:8472200-8480800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr4:8472400-8479800	Weak transcription	Primary B cells from cord blood	blood
19	chr4:8472600-8480000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr4:8473600-8501400	Weak transcription	Brain Substantia Nigra	brain
21	chr4:8474600-8480600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:8474800-8479800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:8475000-8480200	Weak transcription	K562	blood
24	chr4:8475200-8480000	Weak transcription	HSMM	muscle
25	chr4:8475400-8480400	Strong transcription	Spleen	Spleen
26	chr4:8475600-8481400	Strong transcription	Fetal Brain Female	brain
27	chr4:8475600-8491400	Weak transcription	Aorta	Aorta
28	chr4:8475800-8480200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr4:8475800-8480400	Weak transcription	Small Intestine	intestine
30	chr4:8475800-8481200	Weak transcription	NHLF	lung
31	chr4:8475800-8491800	Weak transcription	Colon Smooth Muscle	Colon
32	chr4:8476000-8480800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:8476000-8481400	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr4:8476200-8480600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:8476200-8480600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr4:8476200-8481800	Strong transcription	Fetal Stomach	stomach
37	chr4:8476400-8480200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr4:8476400-8481400	Strong transcription	Right Ventricle	heart
39	chr4:8476600-8481200	Genic enhancers	Placenta	Placenta
40	chr4:8476600-8481400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:8476600-8481400	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr4:8476600-8481400	Strong transcription	Lung	lung
43	chr4:8476600-8481800	Strong transcription	Fetal Muscle Trunk	muscle
44	chr4:8476800-8479600	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr4:8476800-8479600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr4:8476800-8479600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr4:8476800-8479600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:8476800-8479600	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr4:8476800-8480000	Strong transcription	Gastric	stomach
50	chr4:8476800-8480200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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