Variant report

Variant	rs28610962
Chromosome Location	chr1:242136251-242136252
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs2013779	0.81[EUR][1000 genomes]
rs28374104	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28510465	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28613618	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28644381	0.80[ASN][1000 genomes]
rs28656906	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28667776	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28709559	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv948409	chr1:241830086-242489705	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1008300	chr1:241886514-242171611	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1008886	chr1:242015591-242176983	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv2750830	chr1:242025098-242303357	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	esv2750831	chr1:242025098-242332959	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1002309	chr1:242042242-242295635	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv870442	chr1:242105882-242136576	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
10	nsv947475	chr1:242119659-242136347	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
11	esv3353742	chr1:242129501-242179261	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:242121400-242161800	Weak transcription	Right Atrium	heart
2	chr1:242129800-242141600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:242134800-242138000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:242135000-242137600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:242135800-242136400	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr1:242135800-242136400	Enhancers	Fetal Muscle Leg	muscle
7	chr1:242135800-242136400	Enhancers	HSMMtube	muscle
8	chr1:242135800-242136800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:242135800-242136800	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr1:242135800-242136800	Enhancers	HSMM	muscle
11	chr1:242135800-242137000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:242135800-242137000	Enhancers	NH-A	brain
13	chr1:242135800-242137200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:242135800-242137600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:242135800-242137600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr1:242136000-242136400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr1:242136000-242136400	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr1:242136000-242136400	Enhancers	Fetal Brain Male	brain
19	chr1:242136000-242136400	Enhancers	Fetal Muscle Trunk	muscle
20	chr1:242136000-242136400	Enhancers	Placenta Amnion	Placenta Amnion
21	chr1:242136000-242136400	Enhancers	NHDF-Ad	bronchial
22	chr1:242136000-242136400	Enhancers	Osteobl	bone
23	chr1:242136000-242136600	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr1:242136000-242136600	Enhancers	Brain Germinal Matrix	brain
25	chr1:242136000-242136800	Enhancers	Muscle Satellite Cultured Cells	--
26	chr1:242136000-242137200	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr1:242136200-242136400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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