Variant report

Variant	rs1280988
Chromosome Location	chr1:10924710-10924711
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10914701..10916708-chr1:10923191..10926876,3	MCF-7	breast:
2	chr1:10892514..10895346-chr1:10924391..10927017,2	K562	blood:
3	chr1:10923927..10926846-chr1:10929418..10932147,3	K562	blood:
4	chr1:10895615..10898736-chr1:10923813..10928307,5	K562	blood:
5	chr1:10923092..10926846-chr1:10929418..10932147,4	K562	blood:
6	chr1:10834395..10836864-chr1:10924588..10926735,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1280987	0.82[AMR][1000 genomes]
rs1280992	0.90[ASN][1000 genomes]
rs1281002	0.88[ASN][1000 genomes]
rs2790694	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529981	chr1:10697093-11353487	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	esv2757723	chr1:10742502-11055147	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2758921	chr1:10742502-11055147	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv871617	chr1:10858746-10935232	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv871155	chr1:10858746-10998509	Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv1825837	chr1:10887923-11093741	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv832425	chr1:10903845-11122975	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv545406	chr1:10915507-10935232	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1280988	AGTRAP	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10918600-10926600	Weak transcription	Esophagus	oesophagus
2	chr1:10920000-10926800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
3	chr1:10920200-10926800	Bivalent Enhancer	Fetal Muscle Leg	muscle
4	chr1:10921200-10925000	Bivalent Enhancer	Fetal Stomach	stomach
5	chr1:10921200-10926600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:10921600-10926000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:10921600-10926800	Weak transcription	Gastric	stomach
8	chr1:10922000-10925000	Bivalent Enhancer	Fetal Brain Male	brain
9	chr1:10922000-10926200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:10922200-10925600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:10922800-10926800	Weak transcription	Right Atrium	heart
12	chr1:10923000-10926800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:10923400-10925000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:10923600-10925800	Weak transcription	Right Ventricle	heart
15	chr1:10923600-10926600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:10923800-10924800	Enhancers	Liver	Liver
17	chr1:10923800-10925200	Bivalent Enhancer	HepG2	liver
18	chr1:10923800-10926000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
19	chr1:10924000-10924800	Bivalent Enhancer	Fetal Intestine Large	intestine
20	chr1:10924000-10925200	Bivalent Enhancer	Fetal Intestine Small	intestine
21	chr1:10924200-10925000	Bivalent Enhancer	Stomach Mucosa	stomach
22	chr1:10924400-10926800	Weak transcription	Psoas Muscle	Psoas
23	chr1:10924600-10925600	Bivalent Enhancer	Brain Germinal Matrix	brain
24	chr1:10924600-10926000	Weak transcription	Fetal Heart	heart

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