Variant report

Variant	rs10020408
Chromosome Location	chr4:15543011-15543012
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:15533209..15536881-chr4:15540380..15545720,5	K562	blood:

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10003739	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10008875	0.81[ASN][1000 genomes]
rs10008889	0.88[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10012838	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10022610	0.88[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10025837	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10026851	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10030313	0.81[ASN][1000 genomes]
rs10031017	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10034328	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10939621	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs10939628	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1134634	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs11932730	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11933521	0.81[ASN][1000 genomes]
rs11939541	0.82[ASN][1000 genomes]
rs11943107	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11945626	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12508186	0.81[CEU][hapmap]
rs12509029	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12640192	0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs12644327	0.82[ASN][1000 genomes]
rs12645849	0.88[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12649803	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs13104845	0.84[ASN][1000 genomes]
rs13116304	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13121363	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1473166	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16892140	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16892141	0.95[JPT][hapmap]
rs16892152	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2041671	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2110361	0.83[ASN][1000 genomes]
rs2160044	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28419165	0.83[EUR][1000 genomes]
rs28522268	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28528670	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28534607	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28661857	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3822298	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4235380	0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs4279203	0.81[CEU][hapmap]
rs4280723	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4280724	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4393989	0.88[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4583752	0.88[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs4591601	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4698117	0.86[ASN][1000 genomes]
rs4698403	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4698405	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4698408	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56041141	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57526178	0.83[EUR][1000 genomes]
rs59055524	0.83[ASN][1000 genomes]
rs60813847	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62290565	0.82[ASN][1000 genomes]
rs62290605	0.81[ASN][1000 genomes]
rs6449146	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs6449147	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs6449149	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6831286	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6839438	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73125606	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73127647	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs741180	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs759212	0.83[CHB][hapmap];0.82[ASN][1000 genomes]
rs7661102	0.88[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7665390	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7665915	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7682586	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7687010	0.82[ASN][1000 genomes]
rs7697314	0.86[CHB][hapmap];0.88[YRI][hapmap];0.84[ASN][1000 genomes]
rs872678	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9996452	0.91[CHB][hapmap];0.88[YRI][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer 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	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15487400-15570400	Weak transcription	Psoas Muscle	Psoas
2	chr4:15495600-15559400	Weak transcription	HSMMtube	muscle
3	chr4:15502800-15549200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr4:15502800-15577600	Weak transcription	Right Ventricle	heart
5	chr4:15508200-15556400	Weak transcription	Colonic Mucosa	Colon
6	chr4:15508800-15545800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:15509200-15564400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:15509600-15553400	Weak transcription	HepG2	liver
9	chr4:15512000-15580000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr4:15513000-15562400	Weak transcription	Primary B cells from cord blood	blood
11	chr4:15515400-15545200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:15516000-15545600	Weak transcription	Fetal Thymus	thymus
13	chr4:15517800-15551600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr4:15517800-15593600	Weak transcription	HUVEC	blood vessel
15	chr4:15520000-15572400	Weak transcription	Small Intestine	intestine
16	chr4:15520400-15544200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr4:15520600-15544400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr4:15520600-15544600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr4:15520600-15545200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr4:15520600-15553400	Weak transcription	A549	lung
21	chr4:15520800-15545000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr4:15522200-15544600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr4:15526000-15558200	Weak transcription	Spleen	Spleen
24	chr4:15530200-15556600	Weak transcription	HSMM	muscle
25	chr4:15530800-15554600	Weak transcription	Placenta	Placenta
26	chr4:15530800-15554600	Weak transcription	NH-A	brain
27	chr4:15531200-15545200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr4:15531600-15548600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr4:15533000-15554800	Weak transcription	Fetal Brain Male	brain
30	chr4:15537200-15565000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr4:15537400-15621000	Weak transcription	Hela-S3	cervix
32	chr4:15537800-15549000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr4:15538000-15545800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:15538200-15543800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr4:15538600-15546400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:15538600-15548600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr4:15539000-15570400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr4:15539800-15545200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr4:15540000-15555600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:15540200-15543200	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr4:15540200-15543600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr4:15540200-15543600	Weak transcription	Fetal Heart	heart
43	chr4:15540200-15544000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr4:15540200-15544200	Weak transcription	Pancreas	Pancrea
45	chr4:15540200-15547000	Weak transcription	Liver	Liver
46	chr4:15540200-15547000	Weak transcription	Gastric	stomach
47	chr4:15540200-15547400	Weak transcription	Thymus	Thymus
48	chr4:15540200-15548200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr4:15540200-15548800	Weak transcription	Primary T cells from cord blood	blood
50	chr4:15540200-15554400	Weak transcription	Brain Cingulate Gyrus	brain

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