Variant report

Variant	rs72685353
Chromosome Location	chr4:130013730-130013731
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	MXI1	chr4:130012946-130016268	SK-N-SH	brain:	n/a	n/a
2	MYC	chr4:130013591-130013877	H1-hESC	embryonic stem cell:	n/a	n/a
3	RCOR1	chr4:130013701-130015157	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr4:130011739-130015326	IMR90	lung:	n/a	n/a
5	TBP	chr4:130013168-130015332	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr4:130012893-130015801	MCF10A-Er-Src	breast:	n/a	n/a
7	MXI1	chr4:130013134-130015186	GM12878	blood:	n/a	n/a
8	JUN	chr4:130013536-130015192	K562	blood:	n/a	chr4:130014759-130014772
9	POLR2A	chr4:130012999-130015098	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr4:130013657-130015348	PBDE	blood:	n/a	n/a
11	HCFC1	chr4:130013595-130015235	Hela-S3	cervix:	n/a	n/a
12	RFX5	chr4:130013472-130015439	SK-N-SH	brain:	n/a	n/a
13	MXI1	chr4:130013725-130015714	IMR90	lung:	n/a	n/a
14	TBL1XR1	chr4:130013164-130014144	K562	blood:	n/a	n/a
15	E2F4	chr4:130013654-130015299	MCF10A-Er-Src	breast:	n/a	chr4:130014327-130014334 chr4:130014327-130014334 chr4:130014327-130014334 chr4:130014887-130014895

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:

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

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1030830	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12500341	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12503465	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12504200	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12512345	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17416188	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17416706	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1900397	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2044523	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36195612	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3980331	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4975191	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4975293	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4975294	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55925207	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59540486	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6830023	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6845314	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6847784	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72683669	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72683673	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72683684	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72683693	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72685321	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72685324	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72685328	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72685351	1.00[ASN][1000 genomes]
rs72685352	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685365	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7675408	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs921375	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs921376	0.94[ASN][1000 genomes]
rs921377	0.91[EUR][1000 genomes];0.92[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

No data

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	chr4:130011200-130013800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr4:130011200-130016000	Active TSS	NHLF	lung
5	chr4:130011200-130016400	Active TSS	GM12878-XiMat	blood
6	chr4:130011800-130014200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr4:130012000-130013800	Enhancers	Primary T cells fromperipheralblood	blood
8	chr4:130012000-130015000	Active TSS	NHDF-Ad	bronchial
9	chr4:130012200-130013800	Enhancers	Primary B cells from peripheral blood	blood
10	chr4:130012200-130013800	Flanking Active TSS	HUVEC	blood vessel
11	chr4:130012200-130014200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:130012200-130015400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr4:130012200-130015400	Active TSS	A549	lung
14	chr4:130012400-130014000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:130012400-130014200	Weak transcription	Small Intestine	intestine
16	chr4:130012400-130015800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:130012600-130013800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:130012600-130013800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
19	chr4:130012600-130014000	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr4:130012600-130014000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr4:130012600-130014000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr4:130012600-130014000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr4:130012600-130014400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr4:130012600-130015800	Active TSS	Brain Hippocampus Middle	brain
25	chr4:130012800-130013800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr4:130012800-130013800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
27	chr4:130012800-130014000	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr4:130012800-130014000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr4:130012800-130014000	Weak transcription	Stomach Mucosa	stomach
30	chr4:130012800-130014200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr4:130012800-130015400	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr4:130012800-130015400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr4:130012800-130015400	Active TSS	Fetal Muscle Trunk	muscle
34	chr4:130012800-130015400	Active TSS	HMEC	breast
35	chr4:130012800-130015600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:130012800-130018600	Active TSS	K562	blood
37	chr4:130013000-130013800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr4:130013000-130013800	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr4:130013000-130014000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr4:130013000-130014000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr4:130013000-130014000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr4:130013000-130014200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr4:130013000-130014200	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr4:130013000-130014800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr4:130013000-130015000	Active TSS	Rectal Smooth Muscle	rectum
46	chr4:130013000-130015000	Active TSS	Hela-S3	cervix
47	chr4:130013000-130015200	Active TSS	H9 Cell Line	embryonic stem cell
48	chr4:130013000-130015200	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr4:130013000-130015400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr4:130013000-130015400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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