Variant report

Variant	rs10519776
Chromosome Location	chr4:147113322-147113323
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:147113098..147115033-chr4:147118947..147121819,2	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:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-6L6.2.1-2	chr4:147111638-147114339	NONHSAT098666

Extended variants
information (count: 97 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10000407	0.83[EUR][1000 genomes]
rs1079476	0.98[ASN][1000 genomes]
rs11100919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721367	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721873	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723069	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11724307	0.85[EUR][1000 genomes]
rs11725678	0.81[EUR][1000 genomes]
rs11728525	0.85[EUR][1000 genomes]
rs11728609	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11730306	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11733347	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11940961	0.81[EUR][1000 genomes]
rs12152657	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152692	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17021186	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17021217	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17756056	0.83[EUR][1000 genomes]
rs17756234	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17757522	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17757685	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17757715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17758092	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17758396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17758420	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814023	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814065	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814598	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864371	0.81[EUR][1000 genomes]
rs1865531	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2007366	0.83[EUR][1000 genomes]
rs2068009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115796	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115797	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164280	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28393640	0.81[EUR][1000 genomes]
rs28420466	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733458	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733459	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3733460	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3756081	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756082	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756083	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775498	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815967	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3948408	0.81[EUR][1000 genomes]
rs4282199	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4549398	0.81[EUR][1000 genomes]
rs4835286	0.81[EUR][1000 genomes]
rs55736910	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56174047	0.85[EUR][1000 genomes]
rs56279747	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56289966	0.81[EUR][1000 genomes]
rs56333123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56393662	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs62326764	0.81[EUR][1000 genomes]
rs62326797	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62326801	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62326802	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62326804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62326848	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537399	0.81[EUR][1000 genomes]
rs6537400	0.83[EUR][1000 genomes]
rs6537401	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537402	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6537403	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6815527	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816161	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6820462	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821066	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821444	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821479	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821863	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824313	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6832576	0.83[EUR][1000 genomes]
rs6838458	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6839123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6844381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6856647	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6858813	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72727922	0.81[EUR][1000 genomes]
rs72727944	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72727952	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7657269	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7665079	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695415	0.83[EUR][1000 genomes]
rs7745	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919482	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919483	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10519776	RP11-6L6.2	cis	lung	GTEx
rs10519776	RP11-6L6.2	cis	Adipose Subcutaneous	GTEx
rs10519776	RP11-6L6.2	cis	Skin Sun Exposed Lower leg	GTEx
rs10519776	RP11-6L6.2	cis	Nerve Tibial	GTEx

Chromatin state (count:119 , 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	chr4:147103800-147113400	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr4:147103800-147113600	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr4:147103800-147113600	Strong transcription	Primary B cells from cord blood	blood
12	chr4:147103800-147114000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:147103800-147114000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr4:147103800-147114200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:147103800-147117400	Strong transcription	Primary T cells from cord blood	blood
16	chr4:147104000-147113400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr4:147104000-147113600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr4:147104200-147113800	Strong transcription	Fetal Thymus	thymus
19	chr4:147104200-147114200	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr4:147104400-147113800	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr4:147104400-147114000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr4:147104400-147114200	Strong transcription	Fetal Muscle Leg	muscle
23	chr4:147105000-147113400	Strong transcription	Liver	Liver
24	chr4:147105000-147113800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:147105600-147113800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:147105800-147113800	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr4:147107400-147114000	Strong transcription	HSMM	muscle
28	chr4:147107400-147114000	Strong transcription	Osteobl	bone
29	chr4:147107800-147113800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr4:147107800-147113800	Strong transcription	Thymus	Thymus
31	chr4:147107800-147114000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr4:147107800-147114000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr4:147107800-147114000	Strong transcription	Fetal Muscle Trunk	muscle
34	chr4:147108000-147113600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr4:147108000-147113800	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr4:147108000-147114000	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr4:147108000-147114200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr4:147109000-147114000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr4:147109000-147116800	Weak transcription	Brain Substantia Nigra	brain
40	chr4:147109000-147123000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr4:147109400-147114000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr4:147109800-147116800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr4:147109800-147126000	Weak transcription	Aorta	Aorta
44	chr4:147110000-147113400	Weak transcription	Gastric	stomach
45	chr4:147110000-147115400	Weak transcription	Fetal Kidney	kidney
46	chr4:147110000-147116600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:147110400-147113400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr4:147110400-147113400	Weak transcription	Lung	lung
49	chr4:147110400-147115600	Weak transcription	Brain Angular Gyrus	brain
50	chr4:147110400-147116800	Weak transcription	Esophagus	oesophagus

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