Variant report

Variant	rs4938718
Chromosome Location	chr11:119601497-119601498
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr11:119601489-119601840	SH-SY5Y	brain:	n/a	chr11:119601667-119601674
2	RAD21	chr11:119597368-119601907	SK-N-SH	brain:	n/a	chr11:119599960-119599970 chr11:119600188-119600207
3	SMC3	chr11:119597227-119601922	SK-N-SH	brain:	n/a	chr11:119598367-119598374 chr11:119599984-119599994 chr11:119600192-119600206
4	MXI1	chr11:119597064-119601983	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:119600585..119602314-chr11:119925639..119927228,2	MCF-7	breast:

Variant related genes	Relation type
PVRL1	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10790339	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10892444	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10892445	0.85[CEU][hapmap];0.85[GIH][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10892446	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11217426	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs11217429	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11217430	0.87[EUR][1000 genomes]
rs11217433	0.81[AFR][1000 genomes]
rs11217434	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11217437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11217438	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11217440	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11217441	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11217442	0.82[EUR][1000 genomes]
rs11217448	0.81[EUR][1000 genomes]
rs11607610	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12418662	0.81[CEU][hapmap];0.85[GIH][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12421434	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12421466	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12786505	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12793075	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12796806	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12797914	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12800445	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1876795	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2136420	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2136421	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2368936	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs35248712	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3829260	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245206	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4489755	0.85[CEU][hapmap];0.85[GIH][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];0.87[MKK][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4505073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4936496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4938719	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4938720	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58136657	0.82[EUR][1000 genomes]
rs6589770	0.82[EUR][1000 genomes]
rs73006720	0.82[EUR][1000 genomes]
rs7952366	0.81[CEU][hapmap];0.85[GIH][hapmap];0.85[MEX][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9666263	0.81[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898421	chr11:119499014-119631325	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv898422	chr11:119518006-119601779	Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv898423	chr11:119541332-119659753	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1051769	chr11:119572865-119630769	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1037739	chr11:119592989-119630641	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4938718	HSPA8	cis	parietal	SCAN
rs4938718	DDX6	cis	cerebellum	SCAN
rs4938718	SORL1	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:119600800-119601600	Flanking Active TSS	Brain Hippocampus Middle	brain
2	chr11:119600800-119601600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
3	chr11:119600800-119601600	Flanking Active TSS	Pancreas	Pancrea
4	chr11:119600800-119605800	Weak transcription	Brain Germinal Matrix	brain
5	chr11:119601000-119601600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr11:119601000-119601600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr11:119601000-119601600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
8	chr11:119601000-119601600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:119601000-119601600	Enhancers	Placenta Amnion	Placenta Amnion
10	chr11:119601000-119601800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr11:119601000-119601800	Bivalent Enhancer	Fetal Muscle Leg	muscle
12	chr11:119601200-119601600	Enhancers	H1 Cell Line	embryonic stem cell
13	chr11:119601200-119601600	Enhancers	H9 Cell Line	embryonic stem cell
14	chr11:119601200-119601600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
15	chr11:119601200-119601600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr11:119601200-119601600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr11:119601200-119601600	Active TSS	Brain Anterior Caudate	brain
18	chr11:119601200-119601600	Enhancers	Duodenum Mucosa	Duodenum
19	chr11:119601200-119601600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
20	chr11:119601200-119601600	Bivalent Enhancer	Fetal Lung	lung
21	chr11:119601200-119601600	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr11:119601200-119601600	Enhancers	Stomach Mucosa	stomach
23	chr11:119601200-119601600	Active TSS	Stomach Smooth Muscle	stomach
24	chr11:119601200-119601600	Enhancers	GM12878-XiMat	blood
25	chr11:119601200-119601800	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr11:119601200-119601800	Enhancers	Brain Angular Gyrus	brain
27	chr11:119601200-119601800	Enhancers	Fetal Intestine Small	intestine
28	chr11:119601200-119602400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr11:119601200-119612000	Weak transcription	Esophagus	oesophagus
30	chr11:119601200-119612200	Weak transcription	Right Atrium	heart
31	chr11:119601400-119601600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
32	chr11:119601400-119601600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr11:119601400-119601600	Flanking Active TSS	Brain Substantia Nigra	brain
34	chr11:119601400-119601800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
35	chr11:119601400-119601800	Bivalent Enhancer	Fetal Intestine Large	intestine
36	chr11:119601400-119601800	Enhancers	Spleen	Spleen
37	chr11:119601400-119602400	Enhancers	Brain Cingulate Gyrus	brain
38	chr11:119601400-119610200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr11:119601400-119612200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr11:119601400-119612200	Weak transcription	HMEC	breast

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