Variant report

Variant	rs3756704
Chromosome Location	chr5:95160294-95160295
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:57)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:57 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr5:95158909-95160619	HepG2	liver:	n/a	n/a
2	POLR2A	chr5:95159317-95160413	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr5:95159308-95160428	Hela-S3	cervix:	n/a	n/a
4	BCLAF1	chr5:95159458-95160310	GM12878	blood:	n/a	n/a
5	POLR2A	chr5:95156822-95160771	GM12891	blood:	n/a	n/a
6	ZKSCAN1	chr5:95159121-95160405	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr5:95156897-95160393	GM12892	blood:	n/a	n/a
8	CHD1	chr5:95156831-95160568	IMR90	lung:	n/a	n/a
9	POLR2A	chr5:95158866-95160544	GM19193	blood:	n/a	n/a
10	CTCF	chr5:95160180-95160330	GM06990	blood:	n/a	n/a
11	SMC3	chr5:95160046-95160342	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr5:95156816-95160353	GM18505	blood:	n/a	n/a
13	POLR2A	chr5:95159157-95160384	HepG2	liver:	n/a	n/a
14	RCOR1	chr5:95156804-95160777	IMR90	lung:	n/a	n/a
15	POLR2A	chr5:95157646-95160475	U87	brain:	n/a	n/a
16	PML	chr5:95159395-95160454	GM12878	blood:	n/a	n/a
17	POLR2A	chr5:95160281-95160297	GM12878	blood:	n/a	n/a
18	POLR2A	chr5:95156795-95160390	GM19099	blood:	n/a	n/a
19	MYBL2	chr5:95158965-95160391	HepG2	liver:	n/a	n/a
20	SMARCC1	chr5:95158214-95160757	Hela-S3	cervix:	n/a	n/a
21	WRNIP1	chr5:95159697-95160659	GM12878	blood:	n/a	n/a
22	POLR2A	chr5:95156904-95160434	GM12878	blood:	n/a	n/a
23	RUNX3	chr5:95159481-95160342	GM12878	blood:	n/a	n/a
24	POLR2A	chr5:95159187-95160481	HCT-116	colon:	n/a	n/a
25	POLR2A	chr5:95159035-95160401	HepG2	liver:	n/a	n/a
26	KAP1	chr5:95159135-95160351	U2OS	brain:	n/a	n/a
27	BHLHE40	chr5:95159087-95160368	HepG2	liver:	n/a	n/a
28	POLR2A	chr5:95156846-95160303	GM18951	blood:	n/a	n/a
29	POLR2A	chr5:95158936-95160364	GM12892	blood:	n/a	n/a
30	POLR2A	chr5:95159106-95160361	HepG2	liver:	n/a	n/a
31	MAX	chr5:95157998-95160848	HCT-116	colon:	n/a	chr5:95160699-95160706
32	POLR2A	chr5:95158163-95160750	HepG2	liver:	n/a	n/a
33	POLR2A	chr5:95159577-95160322	HL-60	blood:	n/a	n/a
34	USF2	chr5:95159464-95160457	Hela-S3	cervix:	n/a	chr5:95159807-95159818
35	POLR2A	chr5:95158929-95160547	Hela-S3	cervix:	n/a	n/a
36	MXI1	chr5:95159338-95160454	Hela-S3	cervix:	n/a	n/a
37	TCF7L2	chr5:95159003-95160765	Hela-S3	cervix:	n/a	n/a
38	TBP	chr5:95159178-95160410	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr5:95159479-95160373	GM12878	blood:	n/a	n/a
40	POLR2A	chr5:95157614-95160302	U87	brain:	n/a	n/a
41	POLR2A	chr5:95159247-95160497	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr5:95157827-95160788	Hela-S3	cervix:	n/a	n/a
43	CTCF	chr5:95160098-95160358	K562	blood:	n/a	n/a
44	ELF1	chr5:95159644-95160327	K562	blood:	n/a	n/a
45	MAX	chr5:95159339-95160539	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr5:95157652-95160475	U87	brain:	n/a	n/a
47	POLR2A	chr5:95157663-95160302	U87	brain:	n/a	n/a
48	MTA3	chr5:95157059-95160533	GM12878	blood:	n/a	n/a
49	RCOR1	chr5:95159158-95160385	HepG2	liver:	n/a	n/a
50	IKZF1	chr5:95159353-95160497	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:94890265..94891768-chr5:95158248..95160600,2	K562	blood:
2	chr5:95157133..95161008-chr5:95170364..95173601,6	MCF-7	breast:
3	chr5:95159650..95161680-chr5:95169175..95170926,2	MCF-7	breast:
4	chr5:95159839..95161506-chr5:95164819..95166390,2	MCF-7	breast:
5	chr5:95156076..95158959-chr5:95159159..95161216,2	MCF-7	breast:
6	chr5:95137694..95139720-chr5:95158837..95160612,2	MCF-7	breast:

No data

Variant related genes	Relation type
GLRX	TF binding region
ENSG00000251000	Chromatin interaction
ENSG00000173221	Chromatin interaction
ENSG00000198677	Chromatin interaction
ENSG00000164291	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10069749	0.90[ASN][1000 genomes]
rs10077757	0.91[ASN][1000 genomes]
rs1047420	0.94[CHB][hapmap]
rs13361485	0.95[ASN][1000 genomes]
rs13361488	0.95[ASN][1000 genomes]
rs2161313	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs248343	1.00[CHB][hapmap]
rs2547996	1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs35234911	0.95[ASN][1000 genomes]
rs3797206	0.86[ASN][1000 genomes]
rs4561	0.94[CHB][hapmap]
rs60868839	0.84[ASN][1000 genomes]
rs6556890	0.93[ASN][1000 genomes]
rs6873668	0.91[ASN][1000 genomes]
rs6875489	0.91[ASN][1000 genomes]
rs7709560	0.89[ASN][1000 genomes]
rs7725607	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs918469	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs918470	0.94[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs9314160	0.94[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs955688	0.94[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830409	chr5:95006686-95204496	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015180	chr5:95134357-95286446	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv462255	chr5:95142817-95168155	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv598961	chr5:95142817-95168155	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv882389	chr5:95144952-95173887	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95153200-95160400	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr5:95157600-95160400	Flanking Active TSS	K562	blood
3	chr5:95158200-95160400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr5:95158400-95160400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr5:95158400-95160400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr5:95158400-95160600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr5:95158400-95160800	Flanking Active TSS	Dnd41	blood
8	chr5:95158600-95160400	Enhancers	H9 Cell Line	embryonic stem cell
9	chr5:95158600-95160400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
10	chr5:95158600-95160400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr5:95158600-95160400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr5:95158600-95160400	Flanking Active TSS	A549	lung
13	chr5:95158600-95160600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:95158600-95160600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr5:95158600-95160600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:95158600-95160600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr5:95158600-95160600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
18	chr5:95158600-95160600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr5:95158600-95160600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr5:95158600-95160800	Enhancers	H1 Cell Line	embryonic stem cell
21	chr5:95158600-95160800	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr5:95158600-95160800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr5:95158600-95160800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr5:95158600-95160800	Flanking Active TSS	Hela-S3	cervix
25	chr5:95158600-95161000	Enhancers	Small Intestine	intestine
26	chr5:95158800-95160400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr5:95158800-95160400	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr5:95158800-95160400	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr5:95158800-95160400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
30	chr5:95158800-95160400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr5:95158800-95160400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr5:95158800-95160400	Flanking Active TSS	GM12878-XiMat	blood
33	chr5:95158800-95160400	Flanking Active TSS	HepG2	liver
34	chr5:95158800-95160600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr5:95158800-95160600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr5:95158800-95160600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:95158800-95160800	Enhancers	Primary B cells from peripheral blood	blood
38	chr5:95158800-95160800	Enhancers	Fetal Heart	heart
39	chr5:95158800-95160800	Enhancers	Left Ventricle	heart
40	chr5:95158800-95160800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr5:95158800-95164800	Enhancers	Fetal Intestine Large	intestine
42	chr5:95159000-95160400	Enhancers	HMEC	breast
43	chr5:95159000-95160600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr5:95159000-95160600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr5:95159000-95160800	Enhancers	Brain Substantia Nigra	brain
46	chr5:95159000-95160800	Enhancers	Right Ventricle	heart
47	chr5:95159200-95160600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr5:95159400-95160600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr5:95159600-95160400	Flanking Active TSS	Colonic Mucosa	Colon
50	chr5:95159600-95160400	Enhancers	Fetal Lung	lung

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