Variant report

Variant	rs56393662
Chromosome Location	chr4:147111620-147111621
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:147103019..147105139-chr4:147110887..147113160,2	K562	blood:
2	chr4:147106019..147107613-chr4:147111595..147114491,2	K562	blood:
3	chr4:147111066..147113636-chr4:147115907..147120334,4	K562	blood:
4	chr4:147111066..147113405-chr4:147115907..147118837,2	K562	blood:

Variant related genes	Relation type
ENSG00000164167	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10519776	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1079476	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11100919	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11721367	0.98[ASN][1000 genomes]
rs11721873	0.98[ASN][1000 genomes]
rs11723069	0.94[ASN][1000 genomes]
rs11728609	0.98[ASN][1000 genomes]
rs11729787	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11730306	0.94[ASN][1000 genomes]
rs11733347	0.98[ASN][1000 genomes]
rs12152657	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12152692	0.98[ASN][1000 genomes]
rs12152709	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17021186	0.98[ASN][1000 genomes]
rs17021217	0.98[ASN][1000 genomes]
rs17756234	0.80[ASN][1000 genomes]
rs17757522	0.98[ASN][1000 genomes]
rs17757685	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17757715	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17758092	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17758396	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17758420	0.98[ASN][1000 genomes]
rs17814023	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17814065	0.98[ASN][1000 genomes]
rs17814503	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17814598	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1865531	0.98[ASN][1000 genomes]
rs2068009	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2115796	0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2115797	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2163171	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2164280	0.98[ASN][1000 genomes]
rs28420466	0.98[ASN][1000 genomes]
rs3733458	0.98[ASN][1000 genomes]
rs3733459	0.92[ASN][1000 genomes]
rs3733460	0.89[ASN][1000 genomes]
rs3756081	0.98[ASN][1000 genomes]
rs3756082	0.98[ASN][1000 genomes]
rs3756083	0.98[ASN][1000 genomes]
rs3775498	0.98[ASN][1000 genomes]
rs3815967	0.98[ASN][1000 genomes]
rs4282199	0.98[ASN][1000 genomes]
rs55736910	0.98[ASN][1000 genomes]
rs56279747	0.98[ASN][1000 genomes]
rs56333123	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs62326797	0.94[ASN][1000 genomes]
rs62326801	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs62326802	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs62326804	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs62326848	0.98[ASN][1000 genomes]
rs6537401	0.98[ASN][1000 genomes]
rs6537402	0.94[ASN][1000 genomes]
rs6537403	0.98[ASN][1000 genomes]
rs6815527	0.98[ASN][1000 genomes]
rs6816161	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6820462	0.98[ASN][1000 genomes]
rs6821066	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6821444	0.98[ASN][1000 genomes]
rs6821479	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6821863	0.98[ASN][1000 genomes]
rs6824313	0.98[ASN][1000 genomes]
rs6838458	0.80[ASN][1000 genomes]
rs6839123	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6839141	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6844381	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6856647	0.80[ASN][1000 genomes]
rs6858813	0.98[ASN][1000 genomes]
rs72727944	0.90[ASN][1000 genomes]
rs72727952	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7657269	0.98[ASN][1000 genomes]
rs7665079	0.98[ASN][1000 genomes]
rs7745	0.98[ASN][1000 genomes]
rs919482	0.98[ASN][1000 genomes]
rs919483	0.82[AMR][1000 genomes];0.98[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	nsv461674	chr4:147047072-147143572	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv595650	chr4:147047072-147143572	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1018859	chr4:147055618-147138397	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs56393662	RP11-6L6.2	cis	lung	GTEx
rs56393662	RP11-6L6.2	cis	Skin Sun Exposed Lower leg	GTEx
rs56393662	RP11-6L6.2	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147097800-147115400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:147098400-147118600	Weak transcription	Colonic Mucosa	Colon
3	chr4:147098600-147113800	Weak transcription	Hela-S3	cervix
4	chr4:147101400-147114000	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr4:147101400-147116200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:147102600-147113800	Strong transcription	Primary B cells from peripheral blood	blood
7	chr4:147103600-147113400	Strong transcription	Primary hematopoietic stem cells	blood
8	chr4:147103600-147114000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr4:147103800-147112800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:147103800-147113400	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr4:147103800-147113600	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr4:147103800-147113600	Strong transcription	Primary B cells from cord blood	blood
13	chr4:147103800-147114000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:147103800-147114000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr4:147103800-147114200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:147103800-147117400	Strong transcription	Primary T cells from cord blood	blood
17	chr4:147104000-147113000	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr4:147104000-147113400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr4:147104000-147113600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr4:147104200-147112200	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr4:147104200-147113200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:147104200-147113200	Strong transcription	Placenta	Placenta
23	chr4:147104200-147113800	Strong transcription	Fetal Thymus	thymus
24	chr4:147104200-147114200	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr4:147104400-147112200	Strong transcription	Fetal Intestine Large	intestine
26	chr4:147104400-147113200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr4:147104400-147113800	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr4:147104400-147114000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr4:147104400-147114200	Strong transcription	Fetal Muscle Leg	muscle
30	chr4:147105000-147113400	Strong transcription	Liver	Liver
31	chr4:147105000-147113800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:147105200-147112800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:147105600-147113800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr4:147105800-147113200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr4:147105800-147113800	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr4:147107200-147112400	Strong transcription	Dnd41	blood
37	chr4:147107200-147113000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr4:147107200-147113000	Strong transcription	Duodenum Mucosa	Duodenum
39	chr4:147107400-147114000	Strong transcription	HSMM	muscle
40	chr4:147107400-147114000	Strong transcription	Osteobl	bone
41	chr4:147107800-147112000	Strong transcription	HepG2	liver
42	chr4:147107800-147112200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
43	chr4:147107800-147112400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:147107800-147112400	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr4:147107800-147113800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr4:147107800-147113800	Strong transcription	Thymus	Thymus
47	chr4:147107800-147114000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr4:147107800-147114000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:147107800-147114000	Strong transcription	Fetal Muscle Trunk	muscle
50	chr4:147108000-147112400	Strong transcription	H1 Cell Line	embryonic stem cell

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