Variant report

Variant	rs9874803
Chromosome Location	chr3:112737787-112737788
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:99)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:99 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:112737462-112738876	GM18505	blood:	n/a	n/a
2	POLR2A	chr3:112737749-112739026	U87	brain:	n/a	n/a
3	POLR2A	chr3:112737668-112738999	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr3:112737347-112738913	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:112737325-112737792	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:112737210-112739083	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr3:112736649-112739006	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:112737122-112738647	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:112737507-112738795	GM12878	blood:	n/a	n/a
10	MXI1	chr3:112736597-112739325	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr3:112737644-112738856	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr3:112737440-112738867	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr3:112737366-112738731	GM12891	blood:	n/a	n/a
14	MYC	chr3:112737773-112739493	A549	lung:	n/a	chr3:112738310-112738320
15	MYC	chr3:112737716-112739051	K562	blood:	n/a	chr3:112738310-112738320
16	POLR2A	chr3:112737352-112738883	ProgFib	skin:	n/a	n/a
17	MYC	chr3:112737777-112738892	Hela-S3	cervix:	n/a	chr3:112738310-112738320
18	FOXA2	chr3:112737671-112738813	A549	lung:	n/a	n/a
19	POLR2A	chr3:112737243-112738878	GM12892	blood:	n/a	n/a
20	POLR2A	chr3:112737427-112738942	Raji	blood:	n/a	n/a
21	SIN3AK20	chr3:112737776-112738763	PANC-1	pancreas:	n/a	n/a
22	MYC	chr3:112737747-112739063	NB4	blood:	n/a	chr3:112738310-112738320
23	POLR2A	chr3:112737204-112738960	GM12892	blood:	n/a	n/a
24	POLR2A	chr3:112737568-112738889	NB4	blood:	n/a	n/a
25	POLR2A	chr3:112737314-112738864	GM19099	blood:	n/a	n/a
26	GABPA	chr3:112737751-112738803	A549	lung:	n/a	chr3:112738311-112738320 chr3:112738262-112738271
27	REST	chr3:112737244-112739184	H1-neurons	neurons:	n/a	chr3:112738589-112738602
28	POLR2A	chr3:112737407-112738869	H1-neurons	neurons:	n/a	n/a
29	POLR2A	chr3:112737531-112739025	HepG2	liver:	n/a	n/a
30	POLR2A	chr3:112737289-112738993	GM12891	blood:	n/a	n/a
31	POLR2A	chr3:112737695-112738867	K562	blood:	n/a	n/a
32	MXI1	chr3:112737350-112738955	GM12878	blood:	n/a	n/a
33	RELA	chr3:112737291-112739103	GM12891	blood:	n/a	n/a
34	POLR2A	chr3:112737287-112738971	GM12892	blood:	n/a	n/a
35	SIN3AK20	chr3:112737718-112739046	MCF-7	breast:	n/a	n/a
36	RFX5	chr3:112737601-112738888	Hela-S3	cervix:	n/a	n/a
37	MXI1	chr3:112737472-112739995	IMR90	lung:	n/a	n/a
38	HCFC1	chr3:112736957-112739914	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr3:112737770-112738865	PANC-1	pancreas:	n/a	n/a
40	POLR2A	chr3:112737779-112738883	GM12892	blood:	n/a	n/a
41	FOXA1	chr3:112737696-112738856	HepG2	liver:	n/a	n/a
42	POLR2A	chr3:112737348-112738745	GM12891	blood:	n/a	n/a
43	POLR2A	chr3:112737729-112738964	SK-N-MC	brain:	n/a	n/a
44	POLR2A	chr3:112737380-112739021	MCF10A-Er-Src	breast:	n/a	n/a
45	POLR2A	chr3:112737347-112738867	GM12878	blood:	n/a	n/a
46	POLR2A	chr3:112737583-112738846	K562	blood:	n/a	n/a
47	POLR2A	chr3:112736657-112738890	MCF10A-Er-Src	breast:	n/a	n/a
48	MAZ	chr3:112737579-112739392	IMR90	lung:	n/a	chr3:112738310-112738320
49	RELA	chr3:112737562-112739123	GM19099	blood:	n/a	n/a
50	MTA3	chr3:112737440-112738277	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:112737385..112738269-chrX:12992853..12993760,2	Hela-S3	cervix:
2	chr3:112726403..112732813-chr3:112735056..112739637,9	MCF-7	breast:
3	chr3:112709706..112712038-chr3:112736780..112739124,2	MCF-7	breast:
4	chr3:112358855..112360949-chr3:112737036..112738900,2	K562	blood:
5	chr3:112358697..112360499-chr3:112735766..112739410,3	MCF-7	breast:
6	chr3:112727442..112729984-chr3:112737783..112739677,2	MCF-7	breast:
7	chr3:112730174..112733803-chr3:112737181..112739606,5	MCF-7	breast:
8	chr3:112708671..112711453-chr3:112735992..112738475,2	K562	blood:
9	chr3:112358680..112360592-chr3:112737016..112739347,2	MCF-7	breast:
10	chr3:112279739..112282135-chr3:112735331..112738696,3	K562	blood:
11	chr3:112708547..112711309-chr3:112736671..112738787,3	MCF-7	breast:
12	chr3:112708559..112710573-chr3:112736590..112739999,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GTPBP8-1	chr3:112737048-112738553	NONHSAT091210

No data

Variant related genes	Relation type
ENSG00000240057	TF binding region
ENSG00000272844	Chromatin interaction
ENSG00000144848	Chromatin interaction
ENSG00000163608	Chromatin interaction
ENSG00000138459	Chromatin interaction
ENSG00000163607	Chromatin interaction
ENSG00000091986	Chromatin interaction
ENSG00000205542	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10934211	0.82[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11718449	0.94[MEX][hapmap]
rs1488189	0.83[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2272393	0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2293560	0.99[ASN][1000 genomes]
rs2293562	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2306857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3872610	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3889123	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682451	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6796453	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7633507	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650656	0.85[CHB][hapmap];0.94[MEX][hapmap]
rs9288967	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9866791	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv1843165	chr3:112628205-112740145	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9874803	C3orf17	cis	cerebellum	SCAN
rs9874803	GTPBP8	cis	multi-tissue	Pritchard
rs9874803	GTPBP8	cis	lymphoblastoid	seeQTL
rs9874803	GTPBP8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112736200-112738800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:112736600-112739000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:112736800-112737800	Flanking Active TSS	Brain Angular Gyrus	brain
4	chr3:112736800-112737800	Flanking Active TSS	Brain Anterior Caudate	brain
5	chr3:112736800-112737800	Flanking Active TSS	Fetal Heart	heart
6	chr3:112736800-112737800	Enhancers	Small Intestine	intestine
7	chr3:112736800-112737800	Flanking Active TSS	Hela-S3	cervix
8	chr3:112736800-112737800	Flanking Active TSS	Osteobl	bone
9	chr3:112736800-112738000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:112736800-112738000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:112736800-112738800	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr3:112737000-112737800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr3:112737000-112737800	Flanking Active TSS	Fetal Lung	lung
14	chr3:112737000-112738000	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr3:112737000-112738000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr3:112737000-112738000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:112737000-112738000	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr3:112737000-112738000	Flanking Active TSS	Brain Substantia Nigra	brain
19	chr3:112737000-112738000	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr3:112737000-112738000	Flanking Active TSS	Dnd41	blood
21	chr3:112737000-112738000	Flanking Active TSS	HUVEC	blood vessel
22	chr3:112737000-112738000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr3:112737000-112738200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr3:112737000-112738200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:112737000-112738200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr3:112737000-112738800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:112737000-112738800	Active TSS	GM12878-XiMat	blood
28	chr3:112737000-112738800	Active TSS	HSMMtube	muscle
29	chr3:112737000-112739000	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr3:112737000-112739000	Active TSS	Psoas Muscle	Psoas
31	chr3:112737000-112739000	Active TSS	Right Ventricle	heart
32	chr3:112737000-112739200	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr3:112737000-112739200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:112737000-112739200	Active TSS	Fetal Muscle Trunk	muscle
35	chr3:112737200-112737800	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr3:112737200-112737800	Flanking Active TSS	Brain Hippocampus Middle	brain
37	chr3:112737200-112737800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr3:112737200-112737800	Flanking Active TSS	Fetal Thymus	thymus
39	chr3:112737200-112737800	Flanking Active TSS	Placenta Amnion	Placenta Amnion
40	chr3:112737200-112738000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr3:112737200-112738000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr3:112737200-112738000	Flanking Active TSS	Liver	Liver
43	chr3:112737200-112738000	Flanking Active TSS	Fetal Muscle Leg	muscle
44	chr3:112737200-112738000	Flanking Active TSS	Rectal Smooth Muscle	rectum
45	chr3:112737200-112738000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr3:112737200-112738600	Active TSS	Fetal Intestine Small	intestine
47	chr3:112737200-112738800	Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr3:112737200-112738800	Active TSS	H1 Cell Line	embryonic stem cell
49	chr3:112737200-112738800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:112737200-112738800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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