Variant report

Variant	rs3806946
Chromosome Location	chr5:96519496-96519497
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:390)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:390 , 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	USF1	chr5:96519306-96519723	K562	blood:	n/a	n/a
3	MAX	chr5:96518661-96519794	H1-hESC	embryonic stem cell:	n/a	n/a
4	ELK4	chr5:96519253-96519733	Hela-S3	cervix:	n/a	chr5:96519578-96519589
5	PAX5	chr5:96518705-96519545	GM12878	blood:	n/a	chr5:96518998-96519007
6	POLR2A	chr5:96517775-96519865	IMR90	lung:	n/a	n/a
7	SPI1	chr5:96519382-96519708	GM12891	blood:	n/a	chr5:96519579-96519586
8	MYC	chr5:96519371-96519705	MCF-7	breast:	n/a	n/a
9	ELF1	chr5:96519220-96519745	A549	lung:	n/a	n/a
10	E2F6	chr5:96518781-96519788	Hela-S3	cervix:	n/a	chr5:96518998-96519007 chr5:96519511-96519520
11	SPI1	chr5:96519395-96519722	GM12878	blood:	n/a	chr5:96519579-96519586
12	HEY1	chr5:96519107-96519717	HepG2	liver:	n/a	n/a
13	HEY1	chr5:96518712-96519728	K562	blood:	n/a	n/a
14	ELK1	chr5:96518788-96519739	K562	blood:	n/a	n/a
15	MYC	chr5:96518686-96519782	K562	blood:	n/a	n/a
16	CREB1	chr5:96518517-96519815	H1-hESC	embryonic stem cell:	n/a	n/a
17	TBL1XR1	chr5:96518662-96519657	GM12878	blood:	n/a	n/a
18	USF1	chr5:96519359-96519707	A549	lung:	n/a	n/a
19	CTCF	chr5:96519360-96519510	SAEC	small airway:	n/a	n/a
20	SIN3AK20	chr5:96518777-96519780	A549	lung:	n/a	n/a
21	USF1	chr5:96519377-96519666	SK-N-SH_RA	brain:	n/a	n/a
22	NFE2	chr5:96519382-96519672	GM12878	blood:	n/a	n/a
23	RCOR1	chr5:96518693-96519909	GM12878	blood:	n/a	n/a
24	TAF1	chr5:96519100-96519694	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr5:96518648-96519752	K562	blood:	n/a	n/a
26	NR2F2	chr5:96518693-96519939	K562	blood:	n/a	n/a
27	POLR2A	chr5:96518508-96519796	GM12892	blood:	n/a	n/a
28	POLR2A	chr5:96518412-96519746	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr5:96518517-96519856	GM12892	blood:	n/a	n/a
30	NFIC	chr5:96518942-96519605	HepG2	liver:	n/a	n/a
31	ATF2	chr5:96518562-96519502	GM12878	blood:	n/a	n/a
32	TEAD4	chr5:96518482-96519817	K562	blood:	n/a	n/a
33	YY1	chr5:96518560-96519769	GM12878	blood:	n/a	n/a
34	CTCF	chr5:96519400-96519550	GM12871	blood:	n/a	n/a
35	TBL1XR1	chr5:96518839-96519684	K562	blood:	n/a	n/a
36	GTF2B	chr5:96519260-96519672	K562	blood:	n/a	n/a
37	POLR2A	chr5:96518550-96519778	HepG2	liver:	n/a	n/a
38	RFX5	chr5:96518724-96519595	HepG2	liver:	n/a	n/a
39	ZNF384	chr5:96518717-96519863	K562	blood:	n/a	n/a
40	POLR2A	chr5:96518596-96519816	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr5:96518510-96519812	Hela-S3	cervix:	n/a	n/a
42	CHD1	chr5:96518682-96519691	GM12878	blood:	n/a	n/a
43	FOXM1	chr5:96518660-96519553	GM12878	blood:	n/a	n/a
44	PAX5	chr5:96518726-96519712	GM12878	blood:	n/a	chr5:96519579-96519588 chr5:96518998-96519007
45	ATF3	chr5:96518825-96519741	A549	lung:	n/a	n/a
46	YY1	chr5:96519136-96519676	A549	lung:	n/a	n/a
47	SIN3AK20	chr5:96518641-96519501	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr5:96518669-96519781	GM15510	blood:	n/a	n/a
49	MAX	chr5:96518809-96519782	HepG2	liver:	n/a	n/a
50	STAT3	chr5:96518796-96519782	GM12878	blood:	n/a	chr5:96519127-96519135

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:96519465-96519515	HCPEpiC	choroid plexus:	n/a
2	chr5:96519465-96519515	BE2_C	brain:	n/a
3	chr5:96519465-96519515	U87	brain:	n/a
4	chr5:96519465-96519515	HepG2	liver:	n/a
5	chr5:96519465-96519515	NHBE	bronchial:	n/a
6	chr5:96519465-96519515	NT2-D1	testis:	n/a
7	chr5:96519465-96519515	CMK	blood:	n/a
8	chr5:96519465-96519515	HRE	kidney:	n/a
9	chr5:96519465-96519515	IMR90	lung:	fetal
10	chr5:96519465-96519515	HRCEpiC	kidney:	n/a
11	chr5:96519465-96519515	AG09309	skin:	n/a
12	chr5:96519465-96519515	RPTEC	kidney:	n/a
13	chr5:96519465-96519515	BJ	skin:	n/a
14	chr5:96519465-96519515	GM12878	blood:	n/a
15	chr5:96519465-96519515	SK-N-SH_RA	brain:	n/a
16	chr5:96519465-96519515	HMEC	breast:	n/a
17	chr5:96519465-96519515	GM06990	blood:	n/a
18	chr5:96519465-96519515	PFSK-1	brain:	n/a
19	chr5:96519465-96519515	AG04449	skin:	fetal
20	chr5:96519465-96519515	GM19239	blood:	n/a
21	chr5:96519465-96519515	ProgFib	skin:	n/a
22	chr5:96519465-96519515	A549	lung:	n/a
23	chr5:96519465-96519515	H1-hESC	embryonic stem cell:	embryo
24	chr5:96519465-96519515	HIPEpiC	eye:	n/a
25	chr5:96519465-96519515	SK-N-MC	brain:	n/a
26	chr5:96519465-96519515	NHDF-neo	bronchial:	n/a
27	chr5:96519465-96519515	NH-A	brain:	n/a
28	chr5:96519465-96519515	HL-60	blood:	n/a
29	chr5:96519465-96519515	SAEC	small airway:	n/a
30	chr5:96519465-96519515	AoSMC	blood vessel:	n/a
31	chr5:96519465-96519515	HUVEC	blood vessel:	n/a
32	chr5:96519465-96519515	Hela-S3	cervix:	n/a
33	chr5:96519465-96519515	HNPCEpiC	eye:	n/a
34	chr5:96519465-96519515	HEK293	kidney:	embryo
35	chr5:96519465-96519515	AG09319	gingival:	n/a
36	chr5:96519465-96519515	ovcar-3	ovarian:	n/a
37	chr5:96519465-96519515	SK-N-SH	brain:	n/a
38	chr5:96519465-96519515	LNCaP	prostate:	n/a
39	chr5:96519465-96519515	MCF10A-Er-Src	breast:	n/a
40	chr5:96519465-96519515	HAEpiC	amniotic membrane:	n/a
41	chr5:96519465-96519515	PrEC	prostate:	n/a
42	chr5:96519465-96519515	GM12891	blood:	n/a
43	chr5:96519465-96519515	HEEpiC	esophagus:	n/a
44	chr5:96519465-96519515	NB4	blood:	n/a
45	chr5:96519465-96519515	HRPEpiC	eye:	n/a
46	chr5:96519465-96519515	HCF	heart:	n/a
47	chr5:96519465-96519515	HCM	heart:	n/a
48	chr5:96519465-96519515	HPAEpiC	pulmonary alveolar:	n/a
49	chr5:96519465-96519515	AG10803	skin:	n/a
50	chr5:96519465-96519515	K562	blood:	n/a

(count:4 , 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	chr5:96517585..96519769-chr5:96537536..96540052,2	MCF-7	breast:

No data

Variant related genes	Relation type
RIOK2	TF binding region
RIOK2	CpG island
ENSG00000123975	Chromatin interaction
ENSG00000251054	Chromatin interaction
ENSG00000206698	Chromatin interaction
ENSG00000265112	Chromatin interaction
ENSG00000248758	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1645200	0.88[ASN][1000 genomes]
rs2431140	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2432090	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2432091	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2432123	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2544770	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2548411	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs27614	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs30998	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs30999	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs31001	0.86[ASN][1000 genomes]
rs3806945	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6896160	0.80[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs731021	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No data

Chromatin state (count:126 , 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	chr5:96517800-96519600	Active TSS	Muscle Satellite Cultured Cells	--
26	chr5:96517800-96519600	Active TSS	Fetal Intestine Large	intestine
27	chr5:96517800-96519600	Active TSS	Fetal Muscle Leg	muscle
28	chr5:96517800-96519800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:96517800-96519800	Active TSS	Placenta Amnion	Placenta Amnion
30	chr5:96517800-96520000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr5:96518000-96519600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr5:96518000-96519600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr5:96518000-96519600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr5:96518000-96519600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr5:96518000-96519600	Active TSS	Fetal Brain Male	brain
36	chr5:96518000-96519600	Active TSS	A549	lung
37	chr5:96518000-96519800	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr5:96518000-96519800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr5:96518000-96519800	Active TSS	Left Ventricle	heart
40	chr5:96518000-96519800	Active TSS	Lung	lung
41	chr5:96518200-96519600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr5:96518200-96519600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr5:96518200-96519600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr5:96518200-96519600	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr5:96518200-96519600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr5:96518200-96519600	Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr5:96518200-96519600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr5:96518200-96519600	Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr5:96518200-96519600	Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr5:96518200-96519600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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