Variant report

Variant	rs1729995
Chromosome Location	chr3:98304467-98304468
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	ARID3A	chr3:98303816-98304523	K562	blood:	n/a	n/a
2	FOS	chr3:98304136-98304494	MCF10A-Er-Src	breast:	n/a	chr3:98304326-98304337
3	FOSL2	chr3:98304071-98304618	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr3:98304168-98304591	K562	blood:	n/a	n/a
5	POLR2A	chr3:98304156-98304512	K562	blood:	n/a	n/a
6	MAFK	chr3:98304178-98304467	K562	blood:	n/a	n/a
7	ZNF143	chr3:98304316-98304500	K562	blood:	n/a	n/a
8	JUND	chr3:98303951-98304674	SK-N-SH	brain:	n/a	chr3:98304326-98304337
9	FOS	chr3:98304172-98304468	HUVEC	blood vessel:	n/a	chr3:98304326-98304337
10	RCOR1	chr3:98303998-98304528	K562	blood:	n/a	n/a
11	EP300	chr3:98304119-98304531	K562	blood:	n/a	n/a
12	TAF1	chr3:98304062-98304516	K562	blood:	n/a	n/a
13	JUND	chr3:98302551-98304714	K562	blood:	n/a	chr3:98304326-98304337
14	TEAD4	chr3:98304110-98304590	K562	blood:	n/a	n/a
15	JUND	chr3:98303954-98304810	HCT-116	colon:	n/a	chr3:98304326-98304337
16	TBP	chr3:98304129-98304650	K562	blood:	n/a	n/a
17	ZEB1	chr3:98304149-98304504	GM12878	blood:	n/a	n/a
18	YY1	chr3:98304152-98304595	HCT-116	colon:	n/a	n/a
19	JUN	chr3:98304144-98304503	K562	blood:	n/a	n/a
20	E2F4	chr3:98304363-98304568	MCF10A-Er-Src	breast:	n/a	n/a
21	FOS	chr3:98304138-98304492	MCF10A-Er-Src	breast:	n/a	chr3:98304326-98304337
22	ATF3	chr3:98304182-98304503	K562	blood:	n/a	n/a
23	JUND	chr3:98304139-98304483	SK-N-SH	brain:	n/a	chr3:98304326-98304337
24	JUN	chr3:98303400-98304661	K562	blood:	n/a	n/a
25	POLR2A	chr3:98304142-98304647	HCT-116	colon:	n/a	n/a
26	STAT3	chr3:98304125-98304482	MCF10A-Er-Src	breast:	n/a	n/a
27	FOSL1	chr3:98304114-98304625	K562	blood:	n/a	chr3:98304326-98304337
28	TCF7L2	chr3:98304309-98304592	MCF-7	breast:	n/a	n/a
29	MAFF	chr3:98304255-98304606	K562	blood:	n/a	n/a
30	SP1	chr3:98303935-98304748	HCT-116	colon:	n/a	n/a
31	MAZ	chr3:98304122-98304537	K562	blood:	n/a	n/a
32	UBTF	chr3:98304159-98304468	K562	blood:	n/a	n/a
33	POLR2A	chr3:98304153-98304751	K562	blood:	n/a	n/a
34	TAL1	chr3:98304230-98304538	K562	blood:	n/a	n/a
35	JUN	chr3:98304129-98304517	K562	blood:	n/a	n/a
36	FOS	chr3:98304133-98304518	MCF10A-Er-Src	breast:	n/a	chr3:98304326-98304337
37	JUND	chr3:98304044-98304808	HCT-116	colon:	n/a	chr3:98304326-98304337
38	HCFC1	chr3:98304323-98304514	K562	blood:	n/a	n/a
39	GATA1	chr3:98304229-98304610	PBDEFetal	blood:	n/a	n/a
40	JUND	chr3:98304170-98304498	H1-hESC	embryonic stem cell:	n/a	chr3:98304326-98304337
41	POLR2A	chr3:98302277-98304732	PBDE	blood:	n/a	n/a
42	FOSL1	chr3:98304161-98304468	K562	blood:	n/a	chr3:98304326-98304337
43	CTCF	chr3:98304177-98304498	K562	blood:	n/a	n/a
44	CBX3	chr3:98304000-98304800	HCT-116	colon:	n/a	n/a
45	POLR2A	chr3:98304065-98304748	HCT-116	colon:	n/a	n/a
46	POLR2A	chr3:98304168-98304528	U87	brain:	n/a	n/a
47	JUND	chr3:98304177-98304510	HepG2	liver:	n/a	chr3:98304326-98304337
48	MAX	chr3:98304213-98304716	K562	blood:	n/a	n/a
49	GATA1	chr3:98302011-98304762	PBDE	blood:	n/a	chr3:98302745-98302755 chr3:98302832-98302849 chr3:98302745-98302754 chr3:98302747-98302754 chr3:98302125-98302132 chr3:98302740-98302761 chr3:98302743-98302756
50	FOSL1	chr3:98303976-98304722	HCT-116	colon:	n/a	chr3:98304326-98304337

No.	Distal block	Cell Line	Cell type
1	chr3:98303079..98305719-chr3:98311231..98314146,3	K562	blood:
2	chr3:98241309..98243234-chr3:98301701..98304609,2	K562	blood:
3	chr3:97689639..97691921-chr3:98303800..98305616,2	K562	blood:
4	chr3:98303079..98306972-chr3:98311108..98314146,5	K562	blood:

Variant related genes	Relation type
CPOX	TF binding region
ENSG00000080822	Chromatin interaction
ENSG00000248839	Chromatin interaction
ENSG00000080819	Chromatin interaction
ENSG00000170854	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10222524	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1350792	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1350793	0.94[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1381090	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1675526	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1675527	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1675528	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1675531	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1729978	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1729980	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2698315	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34330560	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3762654	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3853723	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4558798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[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	nsv528056	chr3:98101101-98317836	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv520503	chr3:98102801-98317836	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv834775	chr3:98170059-98367552	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv997484	chr3:98284283-98371420	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1000357	chr3:98284283-98381473	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv536661	chr3:98286588-98315764	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98287200-98310200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr3:98287400-98310400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr3:98290400-98307600	Weak transcription	Psoas Muscle	Psoas
4	chr3:98292400-98307400	Weak transcription	Fetal Kidney	kidney
5	chr3:98292400-98307600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:98292400-98310400	Weak transcription	Small Intestine	intestine
7	chr3:98292400-98311000	Weak transcription	Fetal Brain Male	brain
8	chr3:98292600-98310200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:98293000-98311800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:98293200-98310400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:98294400-98310400	Weak transcription	Colonic Mucosa	Colon
12	chr3:98294400-98311000	Weak transcription	Stomach Mucosa	stomach
13	chr3:98294600-98308200	Weak transcription	Colon Smooth Muscle	Colon
14	chr3:98294800-98308200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:98294800-98311000	Weak transcription	Esophagus	oesophagus
16	chr3:98295000-98305800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:98295000-98308000	Weak transcription	Brain Germinal Matrix	brain
18	chr3:98295200-98308200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:98295400-98307200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:98295600-98309800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr3:98296000-98310200	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr3:98296200-98310400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:98296400-98308600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:98296400-98310000	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr3:98296600-98311200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:98296800-98309600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr3:98296800-98310800	Weak transcription	NHLF	lung
28	chr3:98297000-98305000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:98297000-98309600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:98297400-98310400	Weak transcription	Hela-S3	cervix
31	chr3:98298200-98310800	Weak transcription	HUVEC	blood vessel
32	chr3:98298600-98307200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr3:98299600-98308200	Weak transcription	Primary B cells from cord blood	blood
34	chr3:98299600-98309000	Weak transcription	Lung	lung
35	chr3:98299600-98311200	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr3:98300000-98308600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr3:98300000-98311200	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr3:98300400-98307600	Weak transcription	Ovary	ovary
39	chr3:98300600-98307400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:98301600-98306800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:98301600-98307800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr3:98301800-98305400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr3:98301800-98310000	Strong transcription	Liver	Liver
44	chr3:98302000-98309800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:98302200-98305400	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:98302400-98305200	Strong transcription	Primary B cells from peripheral blood	blood
47	chr3:98302400-98305200	Genic enhancers	Brain Inferior Temporal Lobe	brain
48	chr3:98302400-98305200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr3:98302400-98305200	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:98302400-98305400	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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