Variant report

Variant	rs6820462
Chromosome Location	chr4:147097424-147097425
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	chr4:147096162..147099903-chr4:147161380..147165203,4	MCF-7	breast:
2	chr4:147095588..147099041-chr4:147101501..147104102,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-6L6.2.1-3	chr4:147097320-147097838	NONHSAT098665

Variant related genes	Relation type
ENSG00000251010	Chromatin interaction
ENSG00000164167	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10017509	0.83[CEU][hapmap]
rs10021707	0.87[YRI][hapmap]
rs10519776	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1079476	0.98[ASN][1000 genomes]
rs11100919	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721367	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721873	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11722991	0.83[CEU][hapmap]
rs11723069	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11724307	0.81[EUR][1000 genomes]
rs11728525	0.81[EUR][1000 genomes]
rs11728609	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729787	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11730306	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11733347	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734320	0.83[CEU][hapmap]
rs11940961	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs12152657	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152692	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152709	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12186313	0.81[CEU][hapmap]
rs17021106	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17021186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17021217	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17021239	0.81[CEU][hapmap]
rs17021241	0.91[CEU][hapmap]
rs17756234	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17757522	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17757685	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17757715	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17758092	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17758396	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17758420	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814023	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814065	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814503	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814598	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864371	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs1865531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865532	0.82[EUR][1000 genomes]
rs2068009	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115796	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115797	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163171	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164280	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28420466	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733458	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3733460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3733461	0.83[CEU][hapmap]
rs3756081	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756082	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756083	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4282199	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835283	0.81[CEU][hapmap]
rs4835284	0.83[CEU][hapmap]
rs4835286	0.91[CEU][hapmap];0.82[CHB][hapmap]
rs55736910	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56174047	0.81[EUR][1000 genomes]
rs56279747	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56333123	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56393662	0.98[ASN][1000 genomes]
rs62326797	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62326801	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62326802	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62326804	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62326848	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537401	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537402	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6537403	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6813969	0.81[CEU][hapmap]
rs6815527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816161	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821066	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821444	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821479	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821863	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824313	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838174	0.84[CEU][hapmap]
rs6838458	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6839123	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839141	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843421	0.81[CEU][hapmap]
rs6844381	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6856647	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6858813	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72727944	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72727952	0.98[ASN][1000 genomes]
rs7657269	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7665079	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919483	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6820462	RP11-6L6.2	cis	Esophagus Muscularis	GTEx
rs6820462	RP11-6L6.2	cis	Whole Blood	GTEx
rs6820462	RP11-6L6.2	cis	lung	GTEx
rs6820462	RP11-6L6.2	cis	Adipose Subcutaneous	GTEx
rs6820462	RP11-6L6.2	cis	Nerve Tibial	GTEx
rs6820462	RP11-6L6.2	cis	Artery Tibial	GTEx
rs6820462	RP11-6L6.2	cis	Skin Sun Exposed Lower leg	GTEx
rs6820462	RP11-6L6.2	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147096200-147098000	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr4:147096200-147098000	Active TSS	Rectal Smooth Muscle	rectum
3	chr4:147096400-147097600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr4:147096400-147097600	Active TSS	Cortex derived primary cultured neurospheres	brain
5	chr4:147096400-147097600	Active TSS	Fetal Brain Male	brain
6	chr4:147096400-147097600	Active TSS	Fetal Brain Female	brain
7	chr4:147096400-147097600	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr4:147096400-147097600	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr4:147096400-147097800	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr4:147096400-147097800	Active TSS	Duodenum Mucosa	Duodenum
11	chr4:147096400-147097800	Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr4:147096400-147097800	Active TSS	NHDF-Ad	bronchial
13	chr4:147096400-147098000	Active TSS	Brain Substantia Nigra	brain
14	chr4:147096400-147098000	Active TSS	A549	lung
15	chr4:147096400-147098000	Active TSS	K562	blood
16	chr4:147096400-147098200	Active TSS	NH-A	brain
17	chr4:147096400-147098400	Active TSS	GM12878-XiMat	blood
18	chr4:147096600-147097600	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr4:147096600-147097600	Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr4:147096600-147097600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
21	chr4:147096600-147097600	Active TSS	Brain Anterior Caudate	brain
22	chr4:147096600-147097600	Active TSS	Brain Hippocampus Middle	brain
23	chr4:147096600-147097600	Active TSS	Fetal Heart	heart
24	chr4:147096600-147097600	Active TSS	Monocytes-CD14+_RO01746	blood
25	chr4:147096600-147097600	Active TSS	Osteobl	bone
26	chr4:147096600-147097800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr4:147096600-147097800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:147096600-147097800	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr4:147096600-147097800	Active TSS	Brain Cingulate Gyrus	brain
30	chr4:147096600-147097800	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr4:147096600-147097800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr4:147096600-147097800	Active TSS	Fetal Intestine Large	intestine
33	chr4:147096600-147097800	Active TSS	Fetal Muscle Trunk	muscle
34	chr4:147096600-147097800	Active TSS	HSMMtube	muscle
35	chr4:147096600-147097800	Active TSS	NHEK	skin
36	chr4:147096600-147098000	Active TSS	H1 Cell Line	embryonic stem cell
37	chr4:147096600-147098000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr4:147096600-147098000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr4:147096600-147098000	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr4:147096600-147098000	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr4:147096600-147098000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr4:147096600-147098000	Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr4:147096600-147098000	Active TSS	Aorta	Aorta
44	chr4:147096600-147098000	Active TSS	Fetal Kidney	kidney
45	chr4:147096600-147098000	Active TSS	Fetal Stomach	stomach
46	chr4:147096600-147098000	Active TSS	Stomach Smooth Muscle	stomach
47	chr4:147096600-147098000	Active TSS	HMEC	breast
48	chr4:147096600-147098000	Active TSS	NHLF	lung
49	chr4:147096600-147098200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr4:147096600-147098200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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