Variant report

Variant	rs2087446
Chromosome Location	chr4:128884610-128884611
allele	A/C
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	BCL11A	chr4:128884249-128884621	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:128884415-128885470	GM12892	blood:	n/a	n/a
3	HEY1	chr4:128884519-128884669	K562	blood:	n/a	n/a
4	HEY1	chr4:128884506-128884931	K562	blood:	n/a	n/a
5	POLR2A	chr4:128884329-128885459	GM12892	blood:	n/a	n/a
6	POLR2A	chr4:128884584-128885167	GM12892	blood:	n/a	n/a
7	BATF	chr4:128884228-128884611	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:128882454..128884712-chr4:128896329..128897892,2	MCF-7	breast:
2	chr4:128884518..128888041-chr4:128980422..128985043,7	MCF-7	breast:
3	chr4:128884064..128888795-chr4:128980591..128984632,7	MCF-7	breast:

Variant related genes	Relation type
C4orf29	TF binding region
ENSG00000138709	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11098940	0.84[EUR][1000 genomes]
rs11735635	0.85[EUR][1000 genomes]
rs12503257	0.81[EUR][1000 genomes]
rs12504266	0.88[EUR][1000 genomes]
rs12504825	0.85[EUR][1000 genomes]
rs12510785	0.86[EUR][1000 genomes]
rs12645068	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12645636	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12649864	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1975878	0.82[ASN][1000 genomes]
rs1993723	0.80[ASN][1000 genomes]
rs2085843	0.82[ASN][1000 genomes]
rs34475529	0.82[ASN][1000 genomes]
rs34625382	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4833393	0.82[EUR][1000 genomes]
rs4834223	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4834225	0.82[ASN][1000 genomes]
rs55798529	0.83[EUR][1000 genomes]
rs62335590	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62335637	0.82[ASN][1000 genomes]
rs6534655	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6534656	0.87[EUR][1000 genomes]
rs6827422	0.82[ASN][1000 genomes]
rs6839292	0.87[EUR][1000 genomes]
rs6846535	0.87[EUR][1000 genomes]
rs6848998	0.82[ASN][1000 genomes]
rs7376138	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs748630	0.88[EUR][1000 genomes]
rs7692740	0.87[EUR][1000 genomes]
rs959822	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879915	chr4:128167093-129150590	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv817326	chr4:128292216-128915201	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv879922	chr4:128554404-128901402	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv879923	chr4:128554404-129068179	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv1801492	chr4:128566686-128934513	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	esv1792644	chr4:128566686-129133826	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	esv1795770	chr4:128566686-129145581	Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
8	esv3431515	chr4:128657260-128932577	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv532740	chr4:128710011-129035335	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	esv3416036	chr4:128782694-129133956	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv1033701	chr4:128803159-129095018	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	nsv1019193	chr4:128810527-128949320	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	esv1841203	chr4:128817558-129043809	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
14	nsv1029890	chr4:128828468-129041302	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
15	esv1817670	chr4:128850073-129012181	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
16	esv1821180	chr4:128850073-129012181	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
17	nsv1018952	chr4:128850790-129082821	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
18	nsv595388	chr4:128853913-129084831	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:128832600-128885200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr4:128835000-128885200	Weak transcription	Brain Hippocampus Middle	brain
3	chr4:128836800-128885200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:128837000-128885800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr4:128837400-128885800	Weak transcription	Colon Smooth Muscle	Colon
6	chr4:128837800-128885200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:128838400-128885200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr4:128838400-128885800	Weak transcription	Brain Angular Gyrus	brain
9	chr4:128838800-128885200	Weak transcription	Right Ventricle	heart
10	chr4:128840000-128885800	Weak transcription	Aorta	Aorta
11	chr4:128840600-128885200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr4:128840800-128885200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr4:128841600-128885200	Weak transcription	Hela-S3	cervix
14	chr4:128841800-128885200	Weak transcription	Gastric	stomach
15	chr4:128842800-128885400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr4:128842800-128885600	Weak transcription	Psoas Muscle	Psoas
17	chr4:128843000-128885200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:128843000-128885200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:128843000-128885200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr4:128843000-128885800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr4:128843000-128885800	Weak transcription	Brain Substantia Nigra	brain
22	chr4:128847600-128885800	Weak transcription	Lung	lung
23	chr4:128847800-128885200	Weak transcription	Fetal Lung	lung
24	chr4:128850800-128885000	Weak transcription	Brain Germinal Matrix	brain
25	chr4:128851400-128885200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr4:128856600-128885200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:128856600-128885800	Weak transcription	Left Ventricle	heart
28	chr4:128858800-128885800	Weak transcription	NHDF-Ad	bronchial
29	chr4:128862600-128885800	Weak transcription	HUVEC	blood vessel
30	chr4:128863400-128884800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr4:128864000-128884800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr4:128865000-128885800	Weak transcription	Small Intestine	intestine
33	chr4:128865800-128884800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr4:128869600-128885800	Weak transcription	Ovary	ovary
35	chr4:128869800-128885800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr4:128870000-128884800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:128870200-128885200	Weak transcription	Adipose Nuclei	Adipose
38	chr4:128870200-128885200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr4:128870200-128885200	Weak transcription	Thymus	Thymus
40	chr4:128870200-128885800	Weak transcription	Osteobl	bone
41	chr4:128870400-128885200	Weak transcription	Brain Anterior Caudate	brain
42	chr4:128870400-128885400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr4:128870800-128884800	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr4:128870800-128885200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr4:128871000-128885200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr4:128871200-128885200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr4:128871400-128885000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr4:128871400-128885200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr4:128871600-128884800	Weak transcription	HMEC	breast
50	chr4:128873000-128885600	Weak transcription	Right Atrium	heart

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