Variant report

Variant	rs72727952
Chromosome Location	chr4:147120448-147120449
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:147116335..147119084-chr4:147119994..147121504,2	MCF-7	breast:
2	chr4:147113098..147115033-chr4:147118947..147121819,2	K562	blood:

Extended variants
information (count: 79 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10519776	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1079476	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11100919	0.94[AFR][1000 genomes];0.85[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];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11730306	0.94[ASN][1000 genomes]
rs11733347	0.98[ASN][1000 genomes]
rs12152657	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12152692	0.98[ASN][1000 genomes]
rs12152709	0.94[AFR][1000 genomes];0.85[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	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17757715	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17758092	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17758396	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17758420	0.98[ASN][1000 genomes]
rs17814023	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17814065	0.98[ASN][1000 genomes]
rs17814503	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17814598	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1865531	0.98[ASN][1000 genomes]
rs2068009	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2115796	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2115797	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2163171	0.94[AFR][1000 genomes];0.85[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];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs56393662	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.85[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];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6820462	0.98[ASN][1000 genomes]
rs6821066	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6821444	0.98[ASN][1000 genomes]
rs6821479	0.85[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];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6839141	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6844381	0.94[AFR][1000 genomes];0.85[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]
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	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv461675	chr4:147116864-147768206	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv595651	chr4:147116864-147768206	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs72727952	RP11-6L6.2	cis	Adipose Subcutaneous	GTEx
rs72727952	RP11-6L6.2	cis	Skin Sun Exposed Lower leg	GTEx
rs72727952	RP11-6L6.2	cis	lung	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147109000-147123000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr4:147109800-147126000	Weak transcription	Aorta	Aorta
3	chr4:147112000-147127200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr4:147112200-147124800	Weak transcription	Spleen	Spleen
5	chr4:147112200-147125200	Weak transcription	Pancreas	Pancrea
6	chr4:147112800-147127600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr4:147113200-147123000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:147113200-147124200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr4:147113400-147124400	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr4:147113600-147121400	Weak transcription	Primary B cells from cord blood	blood
11	chr4:147113800-147124400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr4:147113800-147126400	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr4:147113800-147127400	Weak transcription	Primary B cells from peripheral blood	blood
14	chr4:147114000-147122000	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr4:147114000-147123600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr4:147114000-147125200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr4:147114000-147126000	Weak transcription	Liver	Liver
18	chr4:147114000-147126000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr4:147114000-147127600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr4:147114000-147129200	Weak transcription	Brain Hippocampus Middle	brain
21	chr4:147114000-147132600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr4:147114000-147144800	Weak transcription	Gastric	stomach
23	chr4:147114200-147126000	Weak transcription	Adipose Nuclei	Adipose
24	chr4:147114400-147124000	Weak transcription	GM12878-XiMat	blood
25	chr4:147114600-147125400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:147117000-147124600	Weak transcription	Esophagus	oesophagus
27	chr4:147117400-147126000	Weak transcription	Primary T cells from cord blood	blood
28	chr4:147117800-147123000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:147120400-147120800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast

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