Variant report

Variant	rs3734010
Chromosome Location	chr5:96518792-96518793
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:373)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:373 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr5:96518453-96520006	A549	lung:	n/a	n/a
2	MAX	chr5:96518661-96519794	H1-hESC	embryonic stem cell:	n/a	n/a
3	CEBPB	chr5:96518695-96519427	HepG2	liver:	n/a	chr5:96519083-96519100
4	PAX5	chr5:96518705-96519545	GM12878	blood:	n/a	chr5:96518998-96519007
5	POLR2A	chr5:96517775-96519865	IMR90	lung:	n/a	n/a
6	E2F6	chr5:96518781-96519788	Hela-S3	cervix:	n/a	chr5:96518998-96519007 chr5:96519511-96519520
7	HEY1	chr5:96518712-96519728	K562	blood:	n/a	n/a
8	ELK1	chr5:96518788-96519739	K562	blood:	n/a	n/a
9	MYC	chr5:96518686-96519782	K562	blood:	n/a	n/a
10	YY1	chr5:96518681-96519035	HepG2	liver:	n/a	n/a
11	CREB1	chr5:96518517-96519815	H1-hESC	embryonic stem cell:	n/a	n/a
12	TBL1XR1	chr5:96518662-96519657	GM12878	blood:	n/a	n/a
13	POLR2A	chr5:96518666-96519105	GM12892	blood:	n/a	n/a
14	SIN3AK20	chr5:96518777-96519780	A549	lung:	n/a	n/a
15	POLR2A	chr5:96518598-96519062	ECC-1	luminal epithelium:	n/a	n/a
16	TAF1	chr5:96518695-96519065	GM12891	blood:	n/a	n/a
17	RCOR1	chr5:96518693-96519909	GM12878	blood:	n/a	n/a
18	ATF3	chr5:96518763-96519118	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr5:96518648-96519752	K562	blood:	n/a	n/a
20	NR2F2	chr5:96518693-96519939	K562	blood:	n/a	n/a
21	POLR2A	chr5:96518508-96519796	GM12892	blood:	n/a	n/a
22	POLR2A	chr5:96518412-96519746	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr5:96518517-96519856	GM12892	blood:	n/a	n/a
24	YY1	chr5:96518615-96519407	GM12878	blood:	n/a	n/a
25	ATF2	chr5:96518562-96519502	GM12878	blood:	n/a	n/a
26	MAZ	chr5:96518678-96519085	Hela-S3	cervix:	n/a	n/a
27	TAF1	chr5:96518682-96519037	GM12878	blood:	n/a	n/a
28	TEAD4	chr5:96518482-96519817	K562	blood:	n/a	n/a
29	YY1	chr5:96518560-96519769	GM12878	blood:	n/a	n/a
30	POLR2A	chr5:96518550-96519778	HepG2	liver:	n/a	n/a
31	RFX5	chr5:96518724-96519595	HepG2	liver:	n/a	n/a
32	ZNF384	chr5:96518717-96519863	K562	blood:	n/a	n/a
33	POLR2A	chr5:96518596-96519816	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr5:96518510-96519812	Hela-S3	cervix:	n/a	n/a
35	CHD1	chr5:96518682-96519691	GM12878	blood:	n/a	n/a
36	FOXM1	chr5:96518660-96519553	GM12878	blood:	n/a	n/a
37	YY1	chr5:96518612-96519103	SK-N-SH_RA	brain:	n/a	n/a
38	MYC	chr5:96518788-96519044	HUVEC	blood vessel:	n/a	n/a
39	PAX5	chr5:96518726-96519712	GM12878	blood:	n/a	chr5:96519579-96519588 chr5:96518998-96519007
40	IRF4	chr5:96518633-96519212	GM12878	blood:	n/a	n/a
41	SIN3AK20	chr5:96518641-96519501	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr5:96518556-96519113	H1-neurons	neurons:	n/a	n/a
43	POLR2A	chr5:96518669-96519781	GM15510	blood:	n/a	n/a
44	NFIC	chr5:96518627-96519389	GM12878	blood:	n/a	n/a
45	POLR2A	chr5:96518695-96519656	H1-hESC	embryonic stem cell:	n/a	n/a
46	MYC	chr5:96518680-96519757	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr5:96518660-96519819	PANC-1	pancreas:	n/a	n/a
48	MXI1	chr5:96518558-96519768	HepG2	liver:	n/a	n/a
49	TBP	chr5:96518763-96519775	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr5:96518474-96519785	K562	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:96517799..96519630-chr9:91924359..91927202,2	MCF-7	breast:
2	chr5:96517922..96519748-chr5:96562831..96564407,2	MCF-7	breast:
3	chr5:96508014..96513294-chr5:96513654..96520413,9	K562	blood:
4	chr5:96517103..96519459-chr5:98107837..98111064,3	MCF-7	breast:
5	chr5:96142348..96143873-chr5:96516638..96519268,2	K562	blood:
6	chr5:96142588..96144739-chr5:96517628..96519299,2	MCF-7	breast:
7	chr5:96517585..96519769-chr5:96537536..96540052,2	MCF-7	breast:
8	chr1:21112901..21113842-chr5:96518449..96519338,2	Hela-S3	cervix:
9	chr5:96269896..96271438-chr5:96517931..96519494,2	MCF-7	breast:
10	chr11:62608625..62609592-chr5:96518540..96519360,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000251513	TF binding region
ENSG00000251054	Chromatin interaction
ENSG00000246763	Chromatin interaction
ENSG00000123975	Chromatin interaction
ENSG00000164307	Chromatin interaction
ENSG00000248758	Chromatin interaction
ENSG00000113441	Chromatin interaction
ENSG00000174136	Chromatin interaction
ENSG00000265112	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000127483	Chromatin interaction
ENSG00000206698	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11135491	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2544774	0.94[ASN][1000 genomes]
rs27312	0.84[GIH][hapmap];0.84[MEX][hapmap]
rs316191	0.80[MEX][hapmap]
rs316192	0.80[MEX][hapmap]
rs316214	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs432482	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8654	0.80[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv830412	chr5:96427305-96606619	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1019790	chr5:96471680-96980633	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer 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	24 gene(s)	inside rSNPs	diseases
5	nsv537812	chr5:96471680-96980633	ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv882391	chr5:96496189-96533469	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv882392	chr5:96496189-96546238	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats 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	15 gene(s)	inside rSNPs	diseases
8	nsv882393	chr5:96496189-96567950	Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3734010	RIOK2	cis	multi-tissue	Pritchard
rs3734010	ERAP2	cis	parietal	SCAN
rs3734010	RIOK2	Cis_1M	lymphoblastoid	RTeQTL
rs3734010	RIOK2	cis	lymphoblastoid	seeQTL
rs3734010	RIOK2	cis	cerebellum	SCAN
rs3734010	FAM172A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96516600-96519600	Active TSS	GM12878-XiMat	blood
2	chr5:96516600-96520200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:96517200-96519600	Active TSS	NHLF	lung
4	chr5:96517200-96519800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr5:96517200-96520000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:96517200-96520200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr5:96517400-96519600	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr5:96517400-96519600	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr5:96517400-96519800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr5:96517400-96519800	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr5:96517400-96519800	Active TSS	Gastric	stomach
12	chr5:96517400-96520000	Active TSS	Aorta	Aorta
13	chr5:96517400-96520000	Active TSS	Psoas Muscle	Psoas
14	chr5:96517400-96520000	Active TSS	HSMMtube	muscle
15	chr5:96517600-96519600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:96517600-96519600	Active TSS	HSMM	muscle
17	chr5:96517600-96519800	Active TSS	H1 Cell Line	embryonic stem cell
18	chr5:96517600-96519800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:96517600-96519800	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr5:96517600-96519800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr5:96517600-96519800	Active TSS	Right Atrium	heart
22	chr5:96517600-96520000	Active TSS	Ovary	ovary
23	chr5:96517600-96520000	Active TSS	Right Ventricle	heart
24	chr5:96517600-96520000	Active TSS	NHDF-Ad	bronchial
25	chr5:96517800-96519400	Active TSS	Primary T cells fromperipheralblood	blood
26	chr5:96517800-96519600	Active TSS	Muscle Satellite Cultured Cells	--
27	chr5:96517800-96519600	Active TSS	Fetal Intestine Large	intestine
28	chr5:96517800-96519600	Active TSS	Fetal Muscle Leg	muscle
29	chr5:96517800-96519800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr5:96517800-96519800	Active TSS	Placenta Amnion	Placenta Amnion
31	chr5:96517800-96520000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr5:96518000-96518800	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr5:96518000-96519400	Active TSS	Fetal Muscle Trunk	muscle
34	chr5:96518000-96519600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr5:96518000-96519600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr5:96518000-96519600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr5:96518000-96519600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:96518000-96519600	Active TSS	Fetal Brain Male	brain
39	chr5:96518000-96519600	Active TSS	A549	lung
40	chr5:96518000-96519800	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr5:96518000-96519800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr5:96518000-96519800	Active TSS	Left Ventricle	heart
43	chr5:96518000-96519800	Active TSS	Lung	lung
44	chr5:96518200-96518800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr5:96518200-96519400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr5:96518200-96519400	Active TSS	NH-A	brain
47	chr5:96518200-96519600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr5:96518200-96519600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:96518200-96519600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr5:96518200-96519600	Active TSS	iPS-18 Cell Line	embryonic stem cell

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