Variant report

Variant	rs6958350
Chromosome Location	chr7:25871933-25871934
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:25862249..25865211-chr7:25870561..25873090,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10225976	0.99[EUR][1000 genomes]
rs10232819	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10241659	0.97[EUR][1000 genomes]
rs10261019	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10271088	0.95[EUR][1000 genomes]
rs10271460	0.97[EUR][1000 genomes]
rs10274306	0.97[EUR][1000 genomes]
rs10951112	0.93[ASN][1000 genomes]
rs11770186	0.83[CEU][hapmap]
rs11976790	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535837	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12666961	0.83[CEU][hapmap]
rs12700664	0.81[ASN][1000 genomes]
rs12700666	0.81[ASN][1000 genomes]
rs12700667	0.85[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13231733	0.81[ASN][1000 genomes]
rs1376527	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1451382	0.97[EUR][1000 genomes]
rs1451383	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1451385	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2060765	0.89[EUR][1000 genomes]
rs2893220	0.97[EUR][1000 genomes]
rs3902751	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4722526	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4722527	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4722528	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4722529	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4722530	0.93[ASN][1000 genomes]
rs4722531	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56376645	0.94[EUR][1000 genomes]
rs60643312	0.99[EUR][1000 genomes]
rs61140461	0.97[EUR][1000 genomes]
rs62447896	0.97[EUR][1000 genomes]
rs6461887	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6961848	0.81[ASN][1000 genomes]
rs7782246	0.95[EUR][1000 genomes]
rs7782292	0.97[EUR][1000 genomes]
rs7793216	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7798431	0.97[EUR][1000 genomes]
rs979165	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9987000	0.93[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	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
rs6958350	SKAP2	cis	cerebellum	SCAN
rs6958350	CCDC126	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

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	chr7:25869200-25873000	Enhancers	Fetal Lung	lung
5	chr7:25869400-25872200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr7:25869400-25872200	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr7:25869400-25872400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr7:25869400-25872400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr7:25869400-25872400	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr7:25869600-25873600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr7:25869600-25881800	Weak transcription	Right Atrium	heart
12	chr7:25869800-25872200	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr7:25869800-25872400	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr7:25869800-25872400	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr7:25870000-25872000	Enhancers	Rectal Smooth Muscle	rectum
16	chr7:25870000-25872400	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr7:25870000-25873200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr7:25870000-25873200	Enhancers	Fetal Kidney	kidney
19	chr7:25870200-25872200	Enhancers	Brain Germinal Matrix	brain
20	chr7:25870200-25873200	Enhancers	Brain Anterior Caudate	brain
21	chr7:25870400-25872000	Enhancers	H1 Cell Line	embryonic stem cell
22	chr7:25870600-25872000	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr7:25870600-25873000	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr7:25870600-25874000	Enhancers	Fetal Heart	heart
25	chr7:25870800-25872200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr7:25870800-25872400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr7:25871000-25872000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr7:25871000-25872400	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr7:25871000-25872600	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr7:25871000-25872800	Enhancers	Brain Angular Gyrus	brain
31	chr7:25871000-25872800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr7:25871000-25872800	Enhancers	HUVEC	blood vessel
33	chr7:25871000-25873000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr7:25871200-25872800	Enhancers	Brain Cingulate Gyrus	brain
35	chr7:25871200-25873400	Weak transcription	K562	blood
36	chr7:25871200-25874600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr7:25871200-25885400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr7:25871400-25872000	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr7:25871400-25872000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr7:25871400-25872000	Enhancers	H9 Cell Line	embryonic stem cell
41	chr7:25871400-25872000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr7:25871600-25872000	Flanking Active TSS	Brain Hippocampus Middle	brain
43	chr7:25871600-25872000	Flanking Active TSS	Ovary	ovary
44	chr7:25871600-25872200	Enhancers	Stomach Mucosa	stomach
45	chr7:25871600-25872800	Enhancers	HepG2	liver
46	chr7:25871800-25872000	Active TSS	Stomach Smooth Muscle	stomach
47	chr7:25871800-25872000	Enhancers	NHLF	lung
48	chr7:25871800-25872400	Enhancers	Osteobl	bone
49	chr7:25871800-25872800	Enhancers	Brain Substantia Nigra	brain
50	chr7:25871800-25873000	Enhancers	Colon Smooth Muscle	Colon

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