Variant report

Variant	rs3811448
Chromosome Location	chr1:154516578-154516579
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153963702..153965277-chr1:154515258..154516911,2	K562	blood:
2	chr1:154511865..154514048-chr1:154515510..154518337,2	K562	blood:
3	chr1:154515410..154518296-chr1:154526483..154528570,2	K562	blood:
4	chr1:154297860..154300046-chr1:154515392..154517289,2	K562	blood:
5	chr1:154515311..154517020-chr1:154530616..154532196,2	K562	blood:
6	chr1:154512548..154514839-chr1:154516013..154517620,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHRNB2-1	chr1:154516439-154516586	NONHSAT006621

No data

Variant related genes	Relation type
ENSG00000143515	Chromatin interaction
ENSG00000160714	Chromatin interaction
ENSG00000163239	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10047079	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11490956	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12403537	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12405637	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12406822	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12408461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2229238	0.84[CEU][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs3811449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4072391	0.84[CEU][hapmap];0.89[CHB][hapmap];0.94[GIH][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs41269915	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41308419	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41313910	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4240872	0.94[GIH][hapmap];0.82[MEX][hapmap]
rs4379670	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4390168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4633282	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4639752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57783436	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58348886	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58710275	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58881140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59084843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59239860	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59741504	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59838898	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60092776	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60255122	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60368585	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60498985	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60760897	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60931472	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61275241	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61403567	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61559765	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61698846	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6669229	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6672087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6674171	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6681207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72999415	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72999419	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72999422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73018293	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73020232	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73020234	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73020246	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73023331	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73023339	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73023346	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73023348	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73023349	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7514452	0.80[CEU][hapmap];0.94[GIH][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs7526293	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7551873	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7556449	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[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	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3811448	CDC42SE1	cis	cerebellum	SCAN
rs3811448	LCE3C	cis	cerebellum	SCAN
rs3811448	CDC42SE1	cis	parietal	SCAN
rs3811448	ADAMTSL4	cis	parietal	SCAN
rs3811448	PMF1	cis	cerebellum	SCAN
rs3811448	S100A7A	cis	cerebellum	SCAN
rs3811448	MTMR11	cis	cerebellum	SCAN
rs3811448	TDRD10	cis	lung	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154492800-154521400	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:154497600-154521200	Weak transcription	Spleen	Spleen
3	chr1:154513600-154528400	Weak transcription	Right Atrium	heart
4	chr1:154513800-154517400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:154514200-154519400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:154515400-154521400	Weak transcription	Esophagus	oesophagus
7	chr1:154515800-154516600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
8	chr1:154516000-154516600	Bivalent Enhancer	Placenta	Placenta
9	chr1:154516000-154521400	Weak transcription	Gastric	stomach
10	chr1:154516200-154516600	Enhancers	Lung	lung
11	chr1:154516400-154516800	Enhancers	Pancreas	Pancrea
12	chr1:154516400-154516800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
13	chr1:154516400-154517000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:154516400-154517000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr1:154516400-154520000	Weak transcription	Right Ventricle	heart
16	chr1:154516400-154520800	Weak transcription	Adipose Nuclei	Adipose
17	chr1:154516400-154521200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:154516400-154521200	Weak transcription	HUVEC	blood vessel

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