Variant report

Variant	rs4974220
Chromosome Location	chr3:56601787-56601788
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:56590931..56593644-chr3:56601004..56602846,2	K562	blood:

Variant related genes	Relation type
ENSG00000180376	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10222449	0.82[EUR][1000 genomes]
rs10222462	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1045926	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10865998	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10865999	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10866000	0.85[ASN][1000 genomes]
rs11130536	0.89[ASN][1000 genomes]
rs11130538	0.86[ASN][1000 genomes]
rs11706624	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11715395	0.88[ASN][1000 genomes]
rs11719656	0.81[ASN][1000 genomes]
rs11921326	0.89[ASN][1000 genomes]
rs12488218	0.81[ASN][1000 genomes]
rs12490749	0.89[ASN][1000 genomes]
rs12636392	0.82[EUR][1000 genomes]
rs12636773	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12715490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094666	0.86[ASN][1000 genomes]
rs13097030	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352766	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1388251	0.82[EUR][1000 genomes]
rs1491166	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17056878	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17216740	0.88[ASN][1000 genomes]
rs2004199	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2029464	0.89[ASN][1000 genomes]
rs2035798	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2054987	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2054988	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2291499	0.89[ASN][1000 genomes]
rs2291501	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2317133	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2317245	0.88[ASN][1000 genomes]
rs28407059	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3732512	0.89[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4093514	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4681951	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4681963	0.86[ASN][1000 genomes]
rs4974224	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66529035	0.81[ASN][1000 genomes]
rs6765870	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6774323	0.86[ASN][1000 genomes]
rs6784100	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6785479	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6790915	0.85[EUR][1000 genomes]
rs6798118	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6799576	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6802051	0.89[ASN][1000 genomes]
rs6804262	0.84[ASN][1000 genomes]
rs6805469	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72877266	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7612599	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7626378	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629559	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7647272	0.82[EUR][1000 genomes]
rs9811046	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9820759	0.86[ASN][1000 genomes]
rs9836539	0.98[AFR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9840528	0.85[ASN][1000 genomes]
rs9842283	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9845096	0.88[ASN][1000 genomes]
rs9845655	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9846282	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9858728	0.86[ASN][1000 genomes]
rs9862490	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9881005	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881154	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9881789	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9881961	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9985253	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9985254	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[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	esv3347557	chr3:56466500-56619322	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv876817	chr3:56517253-56649282	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv460557	chr3:56594735-56661320	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv590362	chr3:56594735-56661320	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56592000-56615600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:56592200-56609400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:56592400-56601800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:56592400-56601800	Weak transcription	Lung	lung
5	chr3:56592400-56602000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:56592400-56602800	Weak transcription	Esophagus	oesophagus
7	chr3:56592400-56602800	Weak transcription	Gastric	stomach
8	chr3:56592400-56602800	Weak transcription	Spleen	Spleen
9	chr3:56592400-56603000	Weak transcription	Pancreas	Pancrea
10	chr3:56592400-56607400	Weak transcription	Psoas Muscle	Psoas
11	chr3:56592400-56615600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:56592400-56639800	Weak transcription	Right Ventricle	heart
13	chr3:56592400-56644800	Weak transcription	Small Intestine	intestine
14	chr3:56592600-56601800	Weak transcription	Aorta	Aorta
15	chr3:56592600-56602200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:56592600-56602200	Weak transcription	Brain Germinal Matrix	brain
17	chr3:56592600-56602200	Weak transcription	Fetal Brain Male	brain
18	chr3:56592600-56603000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:56592600-56603800	Weak transcription	Stomach Mucosa	stomach
20	chr3:56592800-56602000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:56592800-56602000	Weak transcription	Brain Angular Gyrus	brain
22	chr3:56592800-56602000	Weak transcription	A549	lung
23	chr3:56592800-56610200	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:56592800-56644600	Weak transcription	Fetal Heart	heart
25	chr3:56593000-56602200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:56593000-56603000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:56593000-56607800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:56593000-56610000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:56593200-56602000	Weak transcription	Brain Substantia Nigra	brain
30	chr3:56593200-56608000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr3:56593200-56609000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr3:56593200-56609600	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr3:56593200-56616400	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:56593400-56602400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr3:56593400-56607600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:56593400-56608600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:56593600-56609800	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr3:56594000-56603000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr3:56594200-56602000	Strong transcription	HUVEC	blood vessel
40	chr3:56594200-56608000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:56594200-56610200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:56594400-56609400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr3:56594800-56604000	Strong transcription	Primary B cells from peripheral blood	blood
44	chr3:56594800-56609000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:56595400-56602000	Weak transcription	Brain Anterior Caudate	brain
46	chr3:56596000-56602200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr3:56596000-56605800	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr3:56596000-56608400	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr3:56596600-56602800	Weak transcription	NHDF-Ad	bronchial
50	chr3:56597200-56609200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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