Variant report

Variant	rs41469349
Chromosome Location	chr7:25870440-25870441
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10225976	0.95[ASN][1000 genomes]
rs10238703	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10241634	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10241659	0.91[ASN][1000 genomes]
rs10242536	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10245353	0.92[EUR][1000 genomes]
rs10260677	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10262483	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10267498	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10271088	0.91[ASN][1000 genomes]
rs10271460	0.91[ASN][1000 genomes]
rs10274306	0.91[ASN][1000 genomes]
rs10282436	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1055144	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10951112	0.94[EUR][1000 genomes]
rs11770186	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12666961	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1451382	0.89[ASN][1000 genomes]
rs1451385	0.83[CEU][hapmap]
rs2391168	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28392961	0.91[EUR][1000 genomes]
rs28473292	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28858973	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2893220	0.91[ASN][1000 genomes]
rs2893221	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35766302	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4141278	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4722530	0.95[EUR][1000 genomes]
rs56376645	0.93[ASN][1000 genomes]
rs57246313	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60643312	0.93[ASN][1000 genomes]
rs61140461	0.91[ASN][1000 genomes]
rs62447896	0.89[ASN][1000 genomes]
rs7782246	0.91[ASN][1000 genomes]
rs7782292	0.91[ASN][1000 genomes]
rs7798002	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7798130	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7798431	0.89[ASN][1000 genomes]
rs9987000	0.95[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs41469349	SKAP2	cis	cerebellum	SCAN
rs41469349	CCDC126	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25868800-25873400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:25869000-25872000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr7:25869000-25874000	Enhancers	Fetal Stomach	stomach
4	chr7:25869200-25871200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:25869200-25871200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:25869200-25873000	Enhancers	Fetal Lung	lung
7	chr7:25869400-25870600	Weak transcription	Fetal Heart	heart
8	chr7:25869400-25871200	Enhancers	Colon Smooth Muscle	Colon
9	chr7:25869400-25871600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr7:25869400-25872200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr7:25869400-25872200	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr7:25869400-25872400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr7:25869400-25872400	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr7:25869400-25872400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr7:25869600-25871400	Weak transcription	Psoas Muscle	Psoas
16	chr7:25869600-25871600	Enhancers	Ovary	ovary
17	chr7:25869600-25873600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr7:25869600-25881800	Weak transcription	Right Atrium	heart
19	chr7:25869800-25870800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr7:25869800-25872200	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr7:25869800-25872400	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr7:25869800-25872400	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr7:25870000-25872000	Enhancers	Rectal Smooth Muscle	rectum
24	chr7:25870000-25872400	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr7:25870000-25873200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr7:25870000-25873200	Enhancers	Fetal Kidney	kidney
27	chr7:25870200-25871000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr7:25870200-25871400	Enhancers	Brain Substantia Nigra	brain
29	chr7:25870200-25871600	Enhancers	Stomach Smooth Muscle	stomach
30	chr7:25870200-25872200	Enhancers	Brain Germinal Matrix	brain
31	chr7:25870200-25873200	Enhancers	Brain Anterior Caudate	brain
32	chr7:25870400-25870800	Weak transcription	Fetal Intestine Small	intestine
33	chr7:25870400-25871000	Bivalent Enhancer	Fetal Brain Male	brain
34	chr7:25870400-25871400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr7:25870400-25872000	Enhancers	H1 Cell Line	embryonic stem cell

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