Variant report

Variant	rs6618
Chromosome Location	chr17:20903068-20903069
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:20901201..20904612-chr17:20905901..20908917,4	MCF-7	breast:
2	chr17:20902261..20904753-chr17:20906540..20909495,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DHRS7B-3	chr17:20903060-20903350	ENSG00000263986.1

Variant related genes	Relation type
ENSG00000124422	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1044420	0.83[AFR][1000 genomes]
rs1045162	0.91[ASN][1000 genomes]
rs1127814	0.91[ASN][1000 genomes]
rs12602058	0.87[ASN][1000 genomes]
rs12943067	0.90[ASN][1000 genomes]
rs12946114	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1531566	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17770614	0.88[ASN][1000 genomes]
rs2054464	0.88[ASN][1000 genomes]
rs2127095	0.88[ASN][1000 genomes]
rs2291034	0.93[ASN][1000 genomes]
rs2364326	0.84[ASN][1000 genomes]
rs4445951	0.89[ASN][1000 genomes]
rs4985814	0.90[ASN][1000 genomes]
rs4985815	0.89[ASN][1000 genomes]
rs4985816	0.90[ASN][1000 genomes]
rs4985959	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985963	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985967	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4985968	0.84[ASN][1000 genomes]
rs4985969	0.84[ASN][1000 genomes]
rs4985970	0.84[ASN][1000 genomes]
rs4985971	0.84[ASN][1000 genomes]
rs56323013	0.90[ASN][1000 genomes]
rs58235085	0.84[ASN][1000 genomes]
rs59543297	0.86[ASN][1000 genomes]
rs59713572	0.87[ASN][1000 genomes]
rs6587111	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587114	0.89[ASN][1000 genomes]
rs719093	0.88[ASN][1000 genomes]
rs7209129	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7216921	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs899340	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9911289	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	esv2751619	chr17:20462908-20914156	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv949097	chr17:20801739-21406355	Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv529759	chr17:20839079-21529632	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
4	nsv827917	chr17:20896100-20961777	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv960442	chr17:20901168-20903702	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6618	RP11-344E13.3	cis	Skin Sun Exposed Lower leg	GTEx
rs6618	RP11-344E13.3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20896600-20906800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr17:20896800-20904200	Weak transcription	Primary T cells from cord blood	blood
3	chr17:20896800-20904800	Weak transcription	Fetal Kidney	kidney
4	chr17:20896800-20905200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:20897000-20903400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr17:20897000-20905200	Weak transcription	Fetal Brain Male	brain
7	chr17:20897200-20904600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr17:20898000-20905000	Weak transcription	Hela-S3	cervix
9	chr17:20899200-20908600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr17:20899800-20904800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr17:20900000-20903200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr17:20900000-20905000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr17:20900200-20904800	Enhancers	Brain Substantia Nigra	brain
14	chr17:20900200-20924000	Strong transcription	Fetal Stomach	stomach
15	chr17:20900400-20903200	Enhancers	Brain Anterior Caudate	brain
16	chr17:20900400-20904800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr17:20900400-20905200	Enhancers	Brain Angular Gyrus	brain
18	chr17:20900400-20906000	Genic enhancers	Stomach Smooth Muscle	stomach
19	chr17:20900600-20903200	Enhancers	Left Ventricle	heart
20	chr17:20900600-20903400	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr17:20900600-20905600	Genic enhancers	Fetal Muscle Leg	muscle
22	chr17:20900600-20907000	Genic enhancers	Fetal Muscle Trunk	muscle
23	chr17:20900600-20932400	Strong transcription	Fetal Intestine Small	intestine
24	chr17:20900800-20903200	Weak transcription	Esophagus	oesophagus
25	chr17:20900800-20925600	Strong transcription	Fetal Brain Female	brain
26	chr17:20900800-20932200	Strong transcription	Brain Germinal Matrix	brain
27	chr17:20901000-20903800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr17:20901200-20903200	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr17:20901200-20903400	Enhancers	Right Atrium	heart
30	chr17:20901200-20903800	Enhancers	Colon Smooth Muscle	Colon
31	chr17:20901400-20904800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr17:20901400-20905600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr17:20901400-20912200	Strong transcription	Primary B cells from cord blood	blood
34	chr17:20901400-20925200	Strong transcription	Fetal Lung	lung
35	chr17:20901400-20932600	Strong transcription	Thymus	Thymus
36	chr17:20901400-20937000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr17:20901600-20903200	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr17:20901600-20903200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr17:20901600-20904000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr17:20901600-20904000	Genic enhancers	Right Ventricle	heart
41	chr17:20901600-20905600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr17:20901600-20905800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr17:20901600-20908800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr17:20901800-20903200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr17:20901800-20903200	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr17:20901800-20903400	Genic enhancers	Adipose Nuclei	Adipose
47	chr17:20901800-20903400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
48	chr17:20901800-20903600	Enhancers	Fetal Heart	heart
49	chr17:20901800-20903800	Genic enhancers	Lung	lung
50	chr17:20901800-20905000	Strong transcription	Rectal Mucosa Donor 31	rectum

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