Variant report

Variant	rs28420466
Chromosome Location	chr4:147099181-147099182
allele	A/G
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	chr4:147098952..147101592-chr4:147130358..147132148,2	K562	blood:

Variant related genes	Relation type
ENSG00000251010	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
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	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721873	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723069	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11724307	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11728525	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11728609	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729787	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11730306	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11733347	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152657	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152692	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152709	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17021106	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17021186	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17021217	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17756234	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17757522	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17757685	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	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814023	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814065	0.80[AMR][1000 genomes];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]
rs1865531	0.96[AFR][1000 genomes];0.96[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	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733458	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733459	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3733460	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3756081	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756082	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756083	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775498	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815967	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4282199	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55736910	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56174047	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56279747	0.80[AMR][1000 genomes];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]
rs62326764	0.80[AMR][1000 genomes]
rs62326797	0.84[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	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537401	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537402	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6537403	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6815527	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816161	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6820462	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821066	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821444	0.80[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	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824313	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6832576	0.80[AMR][1000 genomes]
rs6838458	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6839123	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839141	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6844381	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6856647	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6858813	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72727922	0.80[AMR][1000 genomes]
rs72727944	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72727952	0.98[ASN][1000 genomes]
rs7657269	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7665079	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919482	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919483	0.90[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs28420466	RP11-6L6.2	cis	Nerve Tibial	GTEx
rs28420466	RP11-6L6.2	cis	Thyroid	GTEx
rs28420466	RP11-6L6.2	cis	lung	GTEx
rs28420466	RP11-6L6.2	cis	Whole Blood	GTEx
rs28420466	RP11-6L6.2	cis	Esophagus Muscularis	GTEx
rs28420466	RP11-6L6.2	cis	Adipose Subcutaneous	GTEx
rs28420466	RP11-6L6.2	cis	Artery Tibial	GTEx
rs28420466	RP11-6L6.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147097600-147099200	Weak transcription	Gastric	stomach
2	chr4:147097600-147099200	Weak transcription	Spleen	Spleen
3	chr4:147097600-147108800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:147097800-147099200	Enhancers	Fetal Brain Male	brain
5	chr4:147097800-147099200	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr4:147097800-147099600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr4:147097800-147099600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr4:147097800-147101400	Enhancers	Primary B cells from peripheral blood	blood
9	chr4:147097800-147104200	Weak transcription	Placenta	Placenta
10	chr4:147097800-147104600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr4:147097800-147108600	Weak transcription	HSMMtube	muscle
12	chr4:147097800-147108800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:147097800-147108800	Weak transcription	Esophagus	oesophagus
14	chr4:147097800-147111000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr4:147097800-147115400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr4:147098000-147099600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr4:147098000-147099600	Enhancers	Pancreas	Pancrea
18	chr4:147098000-147102200	Enhancers	Fetal Heart	heart
19	chr4:147098000-147102800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr4:147098200-147099200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr4:147098200-147099200	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr4:147098200-147099200	Enhancers	Fetal Stomach	stomach
23	chr4:147098200-147099200	Enhancers	Fetal Thymus	thymus
24	chr4:147098200-147099400	Enhancers	Thymus	Thymus
25	chr4:147098200-147099600	Enhancers	Small Intestine	intestine
26	chr4:147098200-147101000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr4:147098200-147101200	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr4:147098200-147102000	Enhancers	Brain Hippocampus Middle	brain
29	chr4:147098400-147099200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:147098400-147099200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr4:147098400-147099200	Enhancers	Brain Angular Gyrus	brain
32	chr4:147098400-147099200	Enhancers	Brain Germinal Matrix	brain
33	chr4:147098400-147099200	Enhancers	Fetal Muscle Leg	muscle
34	chr4:147098400-147099200	Weak transcription	Lung	lung
35	chr4:147098400-147099200	Weak transcription	Psoas Muscle	Psoas
36	chr4:147098400-147099400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr4:147098400-147099400	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr4:147098400-147099400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr4:147098400-147099600	Enhancers	Colon Smooth Muscle	Colon
40	chr4:147098400-147099600	Enhancers	Fetal Intestine Small	intestine
41	chr4:147098400-147099600	Enhancers	Ovary	ovary
42	chr4:147098400-147099600	Enhancers	Right Ventricle	heart
43	chr4:147098400-147099800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr4:147098400-147099800	Enhancers	Liver	Liver
45	chr4:147098400-147099800	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr4:147098400-147099800	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr4:147098400-147100000	Enhancers	Brain Cingulate Gyrus	brain
48	chr4:147098400-147100200	Enhancers	Primary T cells fromperipheralblood	blood
49	chr4:147098400-147100600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr4:147098400-147100600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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