Variant report

Variant	rs1541427
Chromosome Location	chr7:68983295-68983296
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10256483	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10257731	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10265122	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10281633	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10950189	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10950190	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11771876	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12155091	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12530810	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12531644	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12538348	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12698802	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12698803	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12698804	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13243683	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs13246613	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17137493	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1981585	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1981586	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2108046	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2865169	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28758447	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35245526	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41862	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41863	0.82[EUR][1000 genomes]
rs41865	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4268006	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55714924	0.89[EUR][1000 genomes]
rs56854903	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6460521	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6944163	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6946622	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975413	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6979168	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73437648	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7785268	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7810187	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023885	chr7:68894896-69158290	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv538915	chr7:68894896-69158290	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv916011	chr7:68942155-69330800	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv5782	chr7:68946883-68991904	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1541427	VKORC1L1	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:68981200-68983400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr7:68981200-68983400	Weak transcription	Fetal Heart	heart
3	chr7:68981400-68983400	Weak transcription	Right Atrium	heart
4	chr7:68982600-68984000	Enhancers	H1 Cell Line	embryonic stem cell
5	chr7:68982800-68984000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:68982800-68984000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
7	chr7:68982800-68984200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr7:68982800-68984200	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr7:68982800-68984600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:68983000-68983400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
11	chr7:68983000-68983400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr7:68983000-68983400	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr7:68983000-68983400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr7:68983000-68983600	Enhancers	Rectal Smooth Muscle	rectum
15	chr7:68983000-68983800	Enhancers	H9 Cell Line	embryonic stem cell
16	chr7:68983000-68983800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr7:68983000-68983800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr7:68983000-68983800	Flanking Active TSS	Brain Cingulate Gyrus	brain
19	chr7:68983000-68983800	Enhancers	Fetal Brain Male	brain
20	chr7:68983000-68984000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr7:68983000-68984000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr7:68983000-68984000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr7:68983000-68984000	Enhancers	Colon Smooth Muscle	Colon
24	chr7:68983000-68984200	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr7:68983000-68984200	Enhancers	Psoas Muscle	Psoas
26	chr7:68983000-68985000	Enhancers	Brain Germinal Matrix	brain
27	chr7:68983200-68983600	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr7:68983200-68983600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr7:68983200-68983600	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr7:68983200-68983600	Flanking Active TSS	Brain Substantia Nigra	brain
31	chr7:68983200-68983800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr7:68983200-68983800	Flanking Active TSS	Brain Angular Gyrus	brain
33	chr7:68983200-68983800	Flanking Active TSS	Brain Anterior Caudate	brain
34	chr7:68983200-68983800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr7:68983200-68983800	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr7:68983200-68984000	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr7:68983200-68984200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr7:68983200-68984200	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr7:68983200-68984200	Enhancers	Fetal Muscle Leg	muscle

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