Variant report

Variant	rs11728895
Chromosome Location	chr4:130013447-130013448
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr4:130012946-130016268	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr4:130011739-130015326	IMR90	lung:	n/a	n/a
3	TBP	chr4:130013168-130015332	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr4:130012893-130015801	MCF10A-Er-Src	breast:	n/a	n/a
5	MAX	chr4:130013084-130013459	GM12878	blood:	n/a	n/a
6	MXI1	chr4:130013134-130015186	GM12878	blood:	n/a	n/a
7	POLR2A	chr4:130013144-130013481	GM12878	blood:	n/a	n/a
8	POLR2A	chr4:130012999-130015098	Hela-S3	cervix:	n/a	n/a
9	WRNIP1	chr4:130012650-130013501	GM12878	blood:	n/a	n/a
10	ZMIZ1	chr4:130013002-130013503	K562	blood:	n/a	n/a
11	ELK1	chr4:130013417-130013448	GM12878	blood:	n/a	n/a
12	TBL1XR1	chr4:130013164-130014144	K562	blood:	n/a	n/a
13	BHLHE40	chr4:130013212-130013602	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:129993871..129996634-chr4:130011774..130013975,2	K562	blood:
2	chr4:130011776..130014103-chr4:130019273..130020805,2	K562	blood:
3	chr4:130012621..130015537-chr4:130015842..130017627,2	K562	blood:
4	chr4:129730340..129733748-chr4:130013373..130016609,5	K562	blood:

No data

Variant related genes	Relation type
C4orf33	TF binding region
ENSG00000077684	Chromatin interaction
ENSG00000151470	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11098995	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11098996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11722717	0.83[ASN][1000 genomes]
rs11723520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11725174	0.83[AFR][1000 genomes]
rs11726460	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11728986	0.83[AFR][1000 genomes]
rs11736968	0.83[AFR][1000 genomes]
rs11737003	0.83[AFR][1000 genomes]
rs11737495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12500480	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12500938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12501507	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12501997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12505609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12509933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13107038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13114398	0.85[CHB][hapmap]
rs13115576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13118479	0.95[ASN][1000 genomes]
rs13124420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13129706	0.95[ASN][1000 genomes]
rs13134769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13142673	0.83[AFR][1000 genomes]
rs13144594	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13146453	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13148505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17014099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17185515	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs17351999	1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs17789626	1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs17790511	0.84[CHB][hapmap]
rs34145504	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34359646	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34514942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34633860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34810794	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35094990	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35363237	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35501727	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35693043	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35961303	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35975200	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3754476	0.83[AFR][1000 genomes]
rs4552476	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62316964	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62316972	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62317936	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62318662	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66737416	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[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	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv534538	chr4:129799138-130431688	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv879931	chr4:129939775-130178102	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11728895	C4orf33	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:130002800-130013800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:130002800-130013800	Weak transcription	Ovary	ovary
3	chr4:130011000-130013600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr4:130011200-130013800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr4:130011200-130016000	Active TSS	NHLF	lung
6	chr4:130011200-130016400	Active TSS	GM12878-XiMat	blood
7	chr4:130011400-130013600	Flanking Active TSS	Dnd41	blood
8	chr4:130011800-130014200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr4:130012000-130013600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr4:130012000-130013800	Enhancers	Primary T cells fromperipheralblood	blood
11	chr4:130012000-130015000	Active TSS	NHDF-Ad	bronchial
12	chr4:130012200-130013600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:130012200-130013800	Enhancers	Primary B cells from peripheral blood	blood
14	chr4:130012200-130013800	Flanking Active TSS	HUVEC	blood vessel
15	chr4:130012200-130014200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:130012200-130015400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr4:130012200-130015400	Active TSS	A549	lung
18	chr4:130012400-130014000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr4:130012400-130014200	Weak transcription	Small Intestine	intestine
20	chr4:130012400-130015800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:130012600-130013600	Flanking Active TSS	Brain Germinal Matrix	brain
22	chr4:130012600-130013600	Flanking Active TSS	Fetal Brain Female	brain
23	chr4:130012600-130013600	Flanking Active TSS	NHEK	skin
24	chr4:130012600-130013800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:130012600-130013800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
26	chr4:130012600-130014000	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr4:130012600-130014000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr4:130012600-130014000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr4:130012600-130014000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr4:130012600-130014400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr4:130012600-130015800	Active TSS	Brain Hippocampus Middle	brain
32	chr4:130012800-130013600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:130012800-130013600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr4:130012800-130013600	Flanking Active TSS	Brain Anterior Caudate	brain
35	chr4:130012800-130013600	Flanking Active TSS	Fetal Thymus	thymus
36	chr4:130012800-130013800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr4:130012800-130013800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
38	chr4:130012800-130014000	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr4:130012800-130014000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr4:130012800-130014000	Weak transcription	Stomach Mucosa	stomach
41	chr4:130012800-130014200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr4:130012800-130015400	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr4:130012800-130015400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr4:130012800-130015400	Active TSS	Fetal Muscle Trunk	muscle
45	chr4:130012800-130015400	Active TSS	HMEC	breast
46	chr4:130012800-130015600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr4:130012800-130018600	Active TSS	K562	blood
48	chr4:130013000-130013600	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr4:130013000-130013600	Flanking Active TSS	Fetal Lung	lung
50	chr4:130013000-130013600	Enhancers	Left Ventricle	heart

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