Variant report

Variant	rs3811741
Chromosome Location	chr4:128803159-128803160
allele	C/T
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:128800019..128803742-chr4:128979765..128984325,9	K562	blood:
2	chr4:128762399..128765265-chr4:128800417..128803235,2	K562	blood:
3	chr4:128799364..128804463-chr4:128885048..128888163,8	K562	blood:
4	chr4:128701911..128705042-chr4:128800160..128804699,6	K562	blood:
5	chr4:128799393..128805047-chr4:128807036..128813369,7	MCF-7	breast:
6	chr4:128802716..128803224-chr4:128886275..128886832,2	MCF-7	breast:
7	chr4:128702203..128705505-chr4:128800773..128804170,4	MCF-7	breast:
8	chr4:128802720..128805276-chr4:128860657..128863099,2	K562	blood:
9	chr4:128701663..128704492-chr4:128800560..128804784,7	MCF-7	breast:
10	chr4:128798970..128804322-chr4:128884774..128888553,10	K562	blood:
11	chr4:128801016..128804523-chr4:128885640..128887927,4	MCF-7	breast:
12	chr4:128800672..128803742-chr4:128979765..128985676,12	K562	blood:

No data

Variant related genes	Relation type
ENSG00000251821	Chromatin interaction
ENSG00000164070	Chromatin interaction
ENSG00000164073	Chromatin interaction
ENSG00000142731	Chromatin interaction
ENSG00000138709	Chromatin interaction
ENSG00000261668	Chromatin interaction
ENSG00000164074	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10024450	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10493147	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10857126	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11098937	0.83[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap]
rs11725843	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11735635	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12503257	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12504266	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12504825	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12510785	0.81[ASN][1000 genomes]
rs13122568	0.81[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap]
rs13127610	0.86[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.89[MKK][hapmap]
rs1380154	0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1380156	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.84[TSI][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1459048	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.81[TSI][hapmap];0.95[YRI][hapmap];0.84[ASN][1000 genomes]
rs1459049	0.83[CHB][hapmap]
rs1459050	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17012739	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1903104	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.81[TSI][hapmap];0.95[YRI][hapmap]
rs2085655	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs2125573	0.83[CHB][hapmap]
rs2305957	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.92[ASN][1000 genomes]
rs3214038	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs3811740	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3816588	0.84[YRI][hapmap]
rs4833383	0.83[CHB][hapmap]
rs4833391	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4834217	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.81[TSI][hapmap]
rs4834224	0.86[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs6534638	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[ASN][1000 genomes]
rs6534647	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6534648	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6534656	0.81[ASN][1000 genomes]
rs6821748	0.84[ASN][1000 genomes]
rs7441217	0.81[ASN][1000 genomes]
rs748630	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.93[MKK][hapmap];0.81[ASN][1000 genomes]
rs7692740	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs769293	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.95[YRI][hapmap]
rs959822	0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9968459	0.90[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879915	chr4:128167093-129150590	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv817326	chr4:128292216-128915201	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv879917	chr4:128478408-128841252	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv879922	chr4:128554404-128901402	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv879923	chr4:128554404-129068179	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	esv1801492	chr4:128566686-128934513	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	esv1792644	chr4:128566686-129133826	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
8	esv1795770	chr4:128566686-129145581	Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
9	esv1793579	chr4:128577439-128871309	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	esv3431515	chr4:128657260-128932577	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
11	nsv532740	chr4:128710011-129035335	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	esv3416036	chr4:128782694-129133956	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
13	nsv1033701	chr4:128803159-129095018	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3811741	LARP2	cis	multi-tissue	Pritchard
rs3811741	LARP1B	cis	parietal	SCAN
rs3811741	PLK4	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:128800400-128803200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:128800400-128803200	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr4:128800600-128803800	Active TSS	GM12878-XiMat	blood
4	chr4:128801000-128803200	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr4:128801000-128803200	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr4:128801000-128803200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:128801000-128803200	Active TSS	Hela-S3	cervix
8	chr4:128801000-128803400	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr4:128801000-128803400	Active TSS	Muscle Satellite Cultured Cells	--
10	chr4:128801000-128803400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:128801000-128803400	Active TSS	A549	lung
12	chr4:128801200-128803200	Active TSS	H9 Cell Line	embryonic stem cell
13	chr4:128801200-128803200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr4:128801200-128803200	Active TSS	Fetal Intestine Large	intestine
15	chr4:128801200-128803200	Active TSS	Fetal Kidney	kidney
16	chr4:128801200-128803200	Active TSS	NHLF	lung
17	chr4:128801200-128803400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:128801200-128803400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:128801200-128803400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:128801400-128803200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:128801400-128803200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:128801400-128803200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:128801400-128803200	Active TSS	Brain Hippocampus Middle	brain
24	chr4:128801400-128803200	Active TSS	Fetal Muscle Leg	muscle
25	chr4:128801400-128803200	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr4:128801400-128803400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr4:128801400-128803600	Active TSS	H1 Cell Line	embryonic stem cell
28	chr4:128802400-128803200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr4:128802600-128803200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr4:128802600-128803200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
31	chr4:128802600-128803200	Flanking Active TSS	Fetal Muscle Trunk	muscle
32	chr4:128802600-128803200	Flanking Active TSS	Fetal Thymus	thymus
33	chr4:128802600-128803200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
34	chr4:128802600-128803200	Flanking Active TSS	Thymus	Thymus
35	chr4:128802600-128803400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr4:128802600-128803400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:128802600-128803400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr4:128802600-128803400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr4:128802600-128803400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr4:128802600-128804000	Transcr. at gene 5' and 3'	Dnd41	blood
41	chr4:128802800-128803200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr4:128802800-128803200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr4:128802800-128803200	Enhancers	Colon Smooth Muscle	Colon
44	chr4:128802800-128803200	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr4:128802800-128803200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr4:128802800-128803200	Flanking Active TSS	Fetal Brain Female	brain
47	chr4:128802800-128803200	Flanking Active TSS	Fetal Lung	lung
48	chr4:128802800-128803200	Flanking Active TSS	Fetal Stomach	stomach
49	chr4:128802800-128803200	Enhancers	Stomach Mucosa	stomach
50	chr4:128802800-128803200	Flanking Active TSS	NH-A	brain

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