Variant report

Variant	rs62058987
Chromosome Location	chr17:20934531-20934532
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:20934273..20942906-chr17:20943761..20949798,22	MCF-7	breast:
2	chr17:20932232..20934940-chr17:20938795..20941578,2	MCF-7	breast:
3	chr17:20916495..20920338-chr17:20933999..20937587,3	K562	blood:
4	chr17:20913654..20920338-chr17:20930133..20937587,8	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DHRS7B-7	chr17:20934173-20935705	l_1417_chr17:20919472-20934581_brain

Variant related genes	Relation type
ENSG00000124422	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10512423	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204329	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11204331	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11541311	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11651500	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11652224	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11653213	0.80[AMR][1000 genomes]
rs11653504	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654801	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11655985	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11656662	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11656874	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11657155	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11658178	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11658671	0.81[ASN][1000 genomes]
rs11869271	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11870338	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16942330	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16962375	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2009757	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2291035	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3785544	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3891644	0.83[ASN][1000 genomes]
rs55675922	0.86[AMR][1000 genomes]
rs62056764	0.81[ASN][1000 genomes]
rs62056768	0.80[AMR][1000 genomes]
rs62056770	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62056771	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62056832	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62058990	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62058991	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62058993	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62059000	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62059001	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs716959	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7217797	0.80[AMR][1000 genomes]
rs7218520	0.82[ASN][1000 genomes]
rs7224752	0.82[ASN][1000 genomes]
rs8079468	0.81[EUR][1000 genomes];0.89[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	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
2	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
3	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20901400-20937000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr17:20901800-20936800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr17:20902000-20935400	Strong transcription	Dnd41	blood
4	chr17:20903400-20940000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:20903600-20938400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr17:20923000-20943800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr17:20929800-20935200	Weak transcription	Fetal Kidney	kidney
8	chr17:20930200-20935600	Strong transcription	GM12878-XiMat	blood
9	chr17:20930600-20935400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr17:20931600-20935400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr17:20931600-20937600	Enhancers	Brain Substantia Nigra	brain
12	chr17:20931800-20935200	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr17:20931800-20935400	Enhancers	Fetal Heart	heart
14	chr17:20931800-20936600	Weak transcription	HUVEC	blood vessel
15	chr17:20931800-20937000	Genic enhancers	HSMM	muscle
16	chr17:20931800-20940200	Enhancers	Brain Cingulate Gyrus	brain
17	chr17:20932000-20935000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr17:20932000-20935000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr17:20932000-20935200	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr17:20932000-20935400	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr17:20932000-20935600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr17:20932000-20936400	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr17:20932000-20936400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr17:20932000-20936600	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr17:20932000-20937400	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr17:20932000-20937400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr17:20932000-20937400	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr17:20932000-20938000	Enhancers	Brain Hippocampus Middle	brain
29	chr17:20932200-20934600	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr17:20932200-20935000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr17:20932200-20935200	Enhancers	Fetal Lung	lung
32	chr17:20932200-20936000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr17:20932200-20936400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr17:20932200-20936400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr17:20932200-20937400	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr17:20932200-20937800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr17:20932200-20941400	Genic enhancers	A549	lung
38	chr17:20932400-20934600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr17:20932400-20935200	Weak transcription	Fetal Thymus	thymus
40	chr17:20932400-20935400	Weak transcription	Fetal Intestine Small	intestine
41	chr17:20932400-20935400	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr17:20932400-20935400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr17:20932400-20935600	Weak transcription	Placenta	Placenta
44	chr17:20932400-20935800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
45	chr17:20932400-20935800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr17:20932400-20936800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr17:20932400-20937200	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr17:20932400-20937400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr17:20932400-20937600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr17:20932400-20938000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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