Variant report

Variant	rs9829573
Chromosome Location	chr3:50387756-50387757
allele	C/T
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	POLR2A	chr3:50387742-50389033	GM18505	blood:	n/a	n/a
2	POLR2A	chr3:50387717-50389490	PBDE	blood:	n/a	n/a
3	STAT5A	chr3:50387499-50389265	GM12878	blood:	n/a	chr3:50388275-50388282 chr3:50389062-50389071 chr3:50389063-50389071 chr3:50389057-50389077 chr3:50389063-50389072 chr3:50389018-50389030 chr3:50389057-50389077 chr3:50389014-50389022
4	MAX	chr3:50387742-50388936	MCF-7	breast:	n/a	n/a
5	RELA	chr3:50387676-50388760	GM15510	blood:	n/a	n/a
6	EP300	chr3:50387646-50388760	HepG2	liver:	n/a	chr3:50388304-50388311
7	E2F6	chr3:50387726-50388713	H1-hESC	embryonic stem cell:	n/a	chr3:50388338-50388353
8	POLR2A	chr3:50387756-50388987	HL-60	blood:	n/a	n/a
9	POLR2A	chr3:50387756-50388862	GM12892	blood:	n/a	n/a
10	MAX	chr3:50387717-50388928	SK-N-SH	brain:	n/a	n/a
11	CHD2	chr3:50387444-50388770	GM12878	blood:	n/a	n/a
12	E2F6	chr3:50387671-50388628	A549	lung:	n/a	chr3:50388338-50388353
13	MAX	chr3:50387713-50388841	A549	lung:	n/a	n/a
14	POLR2A	chr3:50386687-50389553	Hela-S3	cervix:	n/a	n/a
15	ELF1	chr3:50387652-50389293	HCT-116	colon:	n/a	chr3:50389061-50389070 chr3:50388302-50388311 chr3:50388301-50388312 chr3:50388346-50388358 chr3:50389059-50389072 chr3:50389060-50389071 chr3:50389060-50389071 chr3:50388301-50388312
16	SIN3A	chr3:50387642-50388835	H1-hESC	embryonic stem cell:	n/a	chr3:50388331-50388342 chr3:50388343-50388354
17	MAX	chr3:50387560-50389143	HCT-116	colon:	n/a	n/a
18	POLR2A	chr3:50387718-50388862	GM12891	blood:	n/a	n/a
19	MXI1	chr3:50387492-50389324	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr3:50387752-50388785	GM18526	blood:	n/a	n/a
21	POLR2A	chr3:50387147-50389514	K562	blood:	n/a	n/a
22	MXI1	chr3:50387479-50389132	IMR90	lung:	n/a	n/a
23	POLR2A	chr3:50387490-50389111	H1-neurons	neurons:	n/a	n/a
24	MAX	chr3:50387461-50389005	HepG2	liver:	n/a	n/a
25	CREB1	chr3:50387746-50389021	HepG2	liver:	n/a	n/a
26	MAX	chr3:50387530-50389087	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr3:50387651-50389519	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr3:50387652-50389026	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:50387666-50389702	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr3:50387727-50388852	GM19193	blood:	n/a	n/a
31	MAX	chr3:50387689-50388825	A549	lung:	n/a	n/a
32	MAX	chr3:50387694-50388950	MCF-7	breast:	n/a	n/a
33	REST	chr3:50387423-50388996	H1-neurons	neurons:	n/a	n/a
34	POLR2A	chr3:50387593-50389159	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr3:50387735-50388894	GM12891	blood:	n/a	n/a
36	MAX	chr3:50387688-50388866	H1-hESC	embryonic stem cell:	n/a	n/a
37	MAX	chr3:50387649-50389019	ECC-1	luminal epithelium:	n/a	n/a
38	PML	chr3:50387709-50388993	GM12878	blood:	n/a	n/a
39	POLR2A	chr3:50387713-50388752	GM12878	blood:	n/a	n/a
40	MAX	chr3:50387713-50388951	A549	lung:	n/a	n/a
41	MXI1	chr3:50387639-50388835	GM12878	blood:	n/a	n/a
42	MAZ	chr3:50387397-50389279	IMR90	lung:	n/a	n/a
43	POLR2A	chr3:50387612-50388850	GM12892	blood:	n/a	n/a
44	E2F6	chr3:50387658-50388831	H1-hESC	embryonic stem cell:	n/a	chr3:50388338-50388353
45	ELF1	chr3:50387705-50389312	GM12878	blood:	n/a	chr3:50389061-50389070 chr3:50388302-50388311 chr3:50388301-50388312 chr3:50388346-50388358 chr3:50389059-50389072 chr3:50389060-50389071 chr3:50389060-50389071 chr3:50388301-50388312
46	POLR2A	chr3:50387523-50389258	Raji	blood:	n/a	n/a
47	POLR2A	chr3:50387744-50388964	GM19099	blood:	n/a	n/a
48	MAX	chr3:50387559-50388979	HepG2	liver:	n/a	n/a
49	POLR2A	chr3:50387738-50389030	H1-neurons	neurons:	n/a	n/a
50	MYBL2	chr3:50387722-50389191	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:50364156..50366133-chr3:50386766..50389569,2	MCF-7	breast:
2	chr10:70091655..70092326-chr3:50387628..50388415,2	NB4	blood:
3	chr3:50365306..50367781-chr3:50387742..50389755,3	MCF-7	breast:
4	chr3:50381268..50383319-chr3:50387134..50389655,3	MCF-7	breast:
5	chr3:50303783..50306378-chr3:50387690..50389658,2	MCF-7	breast:
6	chr3:50373346..50376603-chr3:50387024..50392661,8	MCF-7	breast:
7	chr3:50386112..50390194-chr3:50392847..50399521,11	MCF-7	breast:
8	chr3:50376891..50380040-chr3:50387225..50390511,3	MCF-7	breast:

Variant related genes	Relation type
ZMYND10	TF binding region
NPRL2	TF binding region
ENSG00000272104	TF binding region
CYB561D2	TF binding region
ENSG00000235058	Chromatin interaction
ENSG00000114383	Chromatin interaction
ENSG00000004838	Chromatin interaction
ENSG00000126062	Chromatin interaction
ENSG00000232352	Chromatin interaction
ENSG00000012171	Chromatin interaction
ENSG00000068028	Chromatin interaction
ENSG00000096746	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs13316958	1.00[AFR][1000 genomes]
rs13321551	1.00[AFR][1000 genomes]
rs13323932	1.00[AFR][1000 genomes]
rs13324545	0.87[AFR][1000 genomes]
rs13327678	1.00[AFR][1000 genomes]
rs9811223	1.00[AFR][1000 genomes]
rs9820116	1.00[AFR][1000 genomes]
rs9825506	1.00[AFR][1000 genomes]
rs9828683	0.87[AFR][1000 genomes]
rs9835838	1.00[AFR][1000 genomes]
rs9849605	0.87[AFR][1000 genomes]
rs9850145	1.00[AFR][1000 genomes]
rs9860546	1.00[AFR][1000 genomes]
rs9864231	0.87[AFR][1000 genomes]
rs9875449	0.89[AFR][1000 genomes]
rs9883977	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
6	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
7	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
8	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
9	nsv834692	chr3:50198485-50393464	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
10	nsv590254	chr3:50243510-50388607	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
11	nsv460531	chr3:50247824-50436827	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
12	nsv590255	chr3:50247824-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
13	nsv876772	chr3:50255305-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
14	nsv590257	chr3:50302830-50393640	Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
15	nsv590256	chr3:50302830-50420554	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
16	nsv876774	chr3:50302830-50436827	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
17	nsv876773	chr3:50302830-50480131	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
18	nsv834693	chr3:50302830-50507964	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
19	nsv876775	chr3:50324672-50504896	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
20	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50386800-50387800	Flanking Active TSS	Fetal Brain Female	brain
2	chr3:50386800-50387800	Enhancers	Small Intestine	intestine
3	chr3:50386800-50388000	Flanking Active TSS	Brain Germinal Matrix	brain
4	chr3:50386800-50388000	Flanking Active TSS	Colonic Mucosa	Colon
5	chr3:50386800-50388200	Flanking Active TSS	GM12878-XiMat	blood
6	chr3:50386800-50388600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:50387000-50387800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:50387000-50387800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
9	chr3:50387000-50387800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr3:50387000-50387800	Enhancers	Spleen	Spleen
11	chr3:50387000-50388000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:50387000-50388000	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr3:50387000-50388000	Flanking Active TSS	HSMM	muscle
14	chr3:50387000-50388200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr3:50387000-50388200	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr3:50387000-50388200	Flanking Active TSS	Duodenum Mucosa	Duodenum
17	chr3:50387000-50388200	Flanking Active TSS	Fetal Muscle Leg	muscle
18	chr3:50387000-50388200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr3:50387000-50388200	Flanking Active TSS	Dnd41	blood
20	chr3:50387000-50388200	Flanking Active TSS	HepG2	liver
21	chr3:50387000-50389400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
22	chr3:50387200-50387800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr3:50387200-50387800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:50387200-50387800	Flanking Active TSS	Brain Angular Gyrus	brain
25	chr3:50387200-50387800	Flanking Active TSS	Brain Cingulate Gyrus	brain
26	chr3:50387200-50387800	Flanking Active TSS	Brain Hippocampus Middle	brain
27	chr3:50387200-50388000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:50387200-50388000	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr3:50387200-50388000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:50387200-50388000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr3:50387200-50388000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:50387200-50388000	Flanking Active TSS	Brain Substantia Nigra	brain
33	chr3:50387200-50388000	Flanking Active TSS	Fetal Stomach	stomach
34	chr3:50387200-50388000	Flanking Active TSS	Stomach Mucosa	stomach
35	chr3:50387200-50388200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:50387200-50388200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:50387200-50388200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr3:50387200-50388200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr3:50387200-50388200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr3:50387200-50388200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:50387200-50388200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr3:50387200-50388200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:50387200-50388200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr3:50387200-50388200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:50387200-50388200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:50387200-50388200	Flanking Active TSS	Liver	Liver
47	chr3:50387200-50388200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr3:50387200-50388200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr3:50387200-50388200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr3:50387200-50388200	Flanking Active TSS	NHLF	lung

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