Variant report

Variant	rs257683
Chromosome Location	chr5:95296026-95296027
allele	A/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	CTCF	chr5:95295621-95296138	K562	blood:	n/a	n/a
2	CTCF	chr5:95296000-95296150	HMEC	breast:	n/a	n/a
3	MXI1	chr5:95295550-95298162	HepG2	liver:	n/a	n/a
4	RAD21	chr5:95295642-95296224	Hela-S3	cervix:	n/a	n/a
5	CTCF	chr5:95295940-95296090	AG04450	lung:	n/a	n/a
6	RAD21	chr5:95295552-95298217	IMR90	lung:	n/a	chr5:95296846-95296859 chr5:95297062-95297075 chr5:95296847-95296861 chr5:95297059-95297078
7	ZKSCAN1	chr5:95295855-95297313	Hela-S3	cervix:	n/a	chr5:95297097-95297110
8	POLR2A	chr5:95294827-95298308	GM12892	blood:	n/a	n/a
9	CTCF	chr5:95295920-95296070	HCFaa	heart:	n/a	n/a
10	RELA	chr5:95294993-95298352	GM12891	blood:	n/a	chr5:95297005-95297014 chr5:95297005-95297014
11	POLR2A	chr5:95294649-95297075	HepG2	liver:	n/a	n/a
12	CHD1	chr5:95295706-95298302	GM12878	blood:	n/a	chr5:95296574-95296584
13	PML	chr5:95295247-95298289	GM12878	blood:	n/a	chr5:95296249-95296257
14	POLR2A	chr5:95294744-95298231	GM12891	blood:	n/a	n/a
15	POLR2A	chr5:95295805-95296095	GM12878	blood:	n/a	n/a
16	POLR2A	chr5:95294626-95298807	GM12892	blood:	n/a	n/a
17	TBP	chr5:95295719-95296124	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr5:95294626-95298519	GM12892	blood:	n/a	n/a
19	POLR2A	chr5:95295651-95298283	GM18951	blood:	n/a	n/a
20	POLR2A	chr5:95293827-95297878	ProgFib	skin:	n/a	n/a
21	POLR2A	chr5:95294579-95298340	GM12878	blood:	n/a	n/a
22	POLR2A	chr5:95293418-95298067	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr5:95295338-95296055	SK-N-SH	brain:	n/a	n/a
24	SMC3	chr5:95295595-95297958	Hela-S3	cervix:	n/a	chr5:95297064-95297074 chr5:95297060-95297074
25	POLR2A	chr5:95293281-95298477	GM12891	blood:	n/a	n/a
26	POLR2A	chr5:95295376-95298425	GM15510	blood:	n/a	n/a
27	CTCF	chr5:95295880-95296030	RPTEC	kidney:	n/a	n/a
28	POLR2A	chr5:95293681-95298523	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr5:95294788-95297231	A549	lung:	n/a	n/a
30	POLR2A	chr5:95295938-95297669	GM12878	blood:	n/a	n/a
31	CTCF	chr5:95295940-95296090	AG04449	skin:	n/a	n/a
32	SMARCB1	chr5:95295610-95298225	Hela-S3	cervix:	n/a	chr5:95296156-95296165
33	MXI1	chr5:95295981-95297324	Hela-S3	cervix:	n/a	n/a
34	CTCF	chr5:95296000-95296150	HAc	cerebellar:	n/a	n/a
35	POLR2A	chr5:95295377-95296570	U87	brain:	n/a	n/a
36	CTCF	chr5:95295940-95296090	NHDF-neo	bronchial:	n/a	n/a
37	POLR2A	chr5:95294916-95298224	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr5:95295362-95297695	GM12891	blood:	n/a	n/a
39	CTCF	chr5:95295940-95296090	GM12873	blood:	n/a	n/a
40	CTCF	chr5:95295316-95297628	SK-N-SH	brain:	n/a	chr5:95297058-95297076 chr5:95297061-95297070 chr5:95297061-95297074
41	POLR2A	chr5:95294709-95297866	Hela-S3	cervix:	n/a	n/a
42	BRCA1	chr5:95295949-95296668	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr5:95295841-95296119	GM12891	blood:	n/a	n/a
44	POLR2A	chr5:95294702-95296246	HepG2	liver:	n/a	n/a
45	WRNIP1	chr5:95293706-95297115	GM12878	blood:	n/a	n/a
46	E2F6	chr5:95295639-95297483	K562	blood:	n/a	chr5:95297196-95297206 chr5:95297056-95297065
47	MAX	chr5:95294946-95297886	Hela-S3	cervix:	n/a	n/a
48	MTA3	chr5:95295399-95296284	GM12878	blood:	n/a	n/a
49	POLR2A	chr5:95293433-95298625	PBDE	blood:	n/a	n/a
50	POLR2A	chr5:95294723-95298270	GM19193	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:95294090..95296695-chr5:95356956..95358736,2	K562	blood:
2	chr5:94979878..94983810-chr5:95295717..95298674,4	K562	blood:
3	chr5:95268201..95271259-chr5:95293634..95296677,4	K562	blood:
4	chr5:95294561..95296390-chr5:95300649..95302787,2	MCF-7	breast:
5	chr5:95265302..95267698-chr5:95294461..95296344,2	K562	blood:
6	chr5:95294835..95302887-chr5:95306601..95313873,11	K562	blood:
7	chr5:95295795..95298001-chr5:95305862..95309802,3	MCF-7	breast:
8	chr5:95284805..95286720-chr5:95295035..95296550,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251314	TF binding region
ENSG00000213716	Chromatin interaction
ENSG00000175449	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11135439	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs154447	1.00[CHB][hapmap]
rs17085164	1.00[ASN][1000 genomes]
rs17463444	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17463911	1.00[ASN][1000 genomes]
rs17464446	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs248339	1.00[CHB][hapmap]
rs248342	1.00[CHB][hapmap]
rs28926194	1.00[ASN][1000 genomes]
rs35129919	1.00[ASN][1000 genomes]
rs60575087	1.00[ASN][1000 genomes]
rs62365987	1.00[ASN][1000 genomes]
rs6556889	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6888777	1.00[ASN][1000 genomes]
rs6891719	1.00[CHB][hapmap];1.00[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	nsv1019566	chr5:95180352-95300677	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2758003	chr5:95231706-95540433	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	esv2759355	chr5:95231706-95540433	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95290600-95296800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
2	chr5:95291400-95296200	Transcr. at gene 5' and 3'	HMEC	breast
3	chr5:95293000-95296600	Transcr. at gene 5' and 3'	NHEK	skin
4	chr5:95293800-95296200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr5:95293800-95296600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr5:95293800-95296800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:95293800-95296800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
8	chr5:95293800-95297800	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr5:95294000-95297400	Bivalent/Poised TSS	HepG2	liver
10	chr5:95294000-95298000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
11	chr5:95294000-95298000	Active TSS	Rectal Smooth Muscle	rectum
12	chr5:95294200-95296200	Transcr. at gene 5' and 3'	NHLF	lung
13	chr5:95294400-95296200	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:95294400-95297800	Active TSS	HSMMtube	muscle
15	chr5:95294400-95298600	Active TSS	Aorta	Aorta
16	chr5:95294600-95296400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:95294600-95298000	Active TSS	Brain Angular Gyrus	brain
18	chr5:95294600-95298200	Active TSS	Fetal Intestine Large	intestine
19	chr5:95294600-95298200	Active TSS	GM12878-XiMat	blood
20	chr5:95294600-95298400	Active TSS	Brain Substantia Nigra	brain
21	chr5:95294800-95296200	Flanking Active TSS	Placenta	Placenta
22	chr5:95294800-95296400	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr5:95294800-95296400	Flanking Active TSS	Fetal Brain Male	brain
24	chr5:95294800-95296400	Flanking Active TSS	K562	blood
25	chr5:95294800-95296600	Flanking Active TSS	Fetal Thymus	thymus
26	chr5:95294800-95297000	Transcr. at gene 5' and 3'	Pancreatic Islets	Pancreatic Islet
27	chr5:95294800-95297000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr5:95295000-95296400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr5:95295000-95298000	Active TSS	Gastric	stomach
30	chr5:95295000-95298400	Active TSS	Colonic Mucosa	Colon
31	chr5:95295000-95298600	Active TSS	Brain Hippocampus Middle	brain
32	chr5:95295200-95296200	Active TSS	Fetal Intestine Small	intestine
33	chr5:95295200-95296200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr5:95295200-95296200	Flanking Active TSS	HUVEC	blood vessel
35	chr5:95295200-95296200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
36	chr5:95295200-95296400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
37	chr5:95295200-95296400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
38	chr5:95295200-95296400	Flanking Active TSS	Fetal Lung	lung
39	chr5:95295200-95298200	Active TSS	Small Intestine	intestine
40	chr5:95295400-95296200	Flanking Active TSS	Placenta Amnion	Placenta Amnion
41	chr5:95295400-95296200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr5:95295400-95296400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr5:95295400-95296400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
44	chr5:95295400-95296600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr5:95295400-95297000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
46	chr5:95295400-95298200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr5:95295400-95298200	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr5:95295400-95298200	Active TSS	Brain Anterior Caudate	brain
49	chr5:95295400-95298400	Active TSS	Pancreas	Pancrea
50	chr5:95295400-95298600	Active TSS	Right Ventricle	heart

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