Variant report

Variant	rs10238703
Chromosome Location	chr7:25882174-25882175
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:25751339..25752861-chr7:25879316..25882224,2	MCF-7	breast:
2	chr7:25878574..25880347-chr7:25882130..25884614,2	K562	blood:
3	chr7:25881505..25883101-chr7:25886166..25887741,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10225976	0.94[ASN][1000 genomes]
rs10241634	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10241659	0.90[ASN][1000 genomes]
rs10242536	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10245353	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10260677	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10262483	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10267498	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10271088	0.90[ASN][1000 genomes]
rs10271460	0.90[ASN][1000 genomes]
rs10274306	0.90[ASN][1000 genomes]
rs10282436	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1055144	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10951112	0.93[EUR][1000 genomes]
rs11770186	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12666961	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1451382	0.91[ASN][1000 genomes]
rs1451385	0.83[CEU][hapmap]
rs2391168	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28392961	0.89[EUR][1000 genomes]
rs28473292	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28858973	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2893220	0.90[ASN][1000 genomes]
rs2893221	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35766302	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4141278	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41469349	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4722530	0.94[EUR][1000 genomes]
rs56376645	0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs57246313	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60643312	0.92[ASN][1000 genomes]
rs61140461	0.90[ASN][1000 genomes]
rs62447896	0.88[ASN][1000 genomes]
rs7782246	0.90[ASN][1000 genomes]
rs7782292	0.90[ASN][1000 genomes]
rs7798002	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7798130	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7798431	0.90[ASN][1000 genomes]
rs9987000	0.94[EUR][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	nsv1016813	chr7:25405859-26150509	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
2	nsv538803	chr7:25405859-26150509	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
3	nsv830928	chr7:25820147-25965014	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10238703	TRIL	cis	cerebellum	SCAN
rs10238703	SKAP2	cis	cerebellum	SCAN
rs10238703	CCDC126	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25871200-25885400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:25872200-25886200	Weak transcription	NHLF	lung
3	chr7:25872400-25885200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr7:25876800-25885000	Weak transcription	Fetal Kidney	kidney
5	chr7:25879200-25883000	Enhancers	Fetal Heart	heart
6	chr7:25879200-25884200	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr7:25879400-25883000	Enhancers	Psoas Muscle	Psoas
8	chr7:25880000-25888800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr7:25880000-25889000	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr7:25880200-25883400	Enhancers	Left Ventricle	heart
11	chr7:25880400-25883800	Weak transcription	Aorta	Aorta
12	chr7:25880400-25885200	Weak transcription	Ovary	ovary
13	chr7:25880600-25882800	Enhancers	Rectal Smooth Muscle	rectum
14	chr7:25881000-25884000	Enhancers	Fetal Muscle Leg	muscle
15	chr7:25881200-25882200	Enhancers	Fetal Stomach	stomach
16	chr7:25881400-25882400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr7:25881400-25882800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:25881400-25882800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr7:25881400-25883800	Enhancers	Colon Smooth Muscle	Colon
20	chr7:25881600-25882200	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr7:25881600-25882600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr7:25881600-25882600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr7:25881600-25882600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr7:25881600-25883000	Enhancers	Stomach Smooth Muscle	stomach
25	chr7:25881600-25883400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr7:25881800-25882200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:25881800-25882200	Enhancers	Adipose Nuclei	Adipose
28	chr7:25881800-25883000	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr7:25881800-25883400	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr7:25881800-25884000	Enhancers	Right Atrium	heart
31	chr7:25881800-25889000	Enhancers	Osteobl	bone
32	chr7:25882000-25882200	Enhancers	NH-A	brain
33	chr7:25882000-25882600	Weak transcription	Fetal Lung	lung
34	chr7:25882000-25882800	Enhancers	H9 Cell Line	embryonic stem cell
35	chr7:25882000-25885400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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