Variant report

Variant	rs28364680
Chromosome Location	chr3:158520011-158520012
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:337)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:337 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr3:158519606-158520037	K562	blood:	n/a	n/a
2	FOSL2	chr3:158519390-158520060	A549	lung:	n/a	n/a
3	POLR2A	chr3:158519012-158520264	HUVEC	blood vessel:	n/a	n/a
4	GATA3	chr3:158519102-158520263	A549	lung:	n/a	n/a
5	GABPA	chr3:158519463-158520208	MCF-7	breast:	n/a	n/a
6	TAF1	chr3:158519535-158520029	H1-neurons	neurons:	n/a	n/a
7	STAT1	chr3:158519508-158520062	GM12878	blood:	n/a	n/a
8	RCOR1	chr3:158519379-158520799	K562	blood:	n/a	n/a
9	CTCF	chr3:158520000-158520150	GM12864	blood:	n/a	n/a
10	POLR2A	chr3:158519357-158520436	GM12891	blood:	n/a	n/a
11	CBX3	chr3:158519477-158520093	K562	blood:	n/a	n/a
12	POLR2A	chr3:158519411-158520339	GM15510	blood:	n/a	n/a
13	POLR2A	chr3:158519457-158520050	SK-N-MC	brain:	n/a	n/a
14	SIN3AK20	chr3:158519314-158520361	MCF-7	breast:	n/a	n/a
15	CHD2	chr3:158519721-158520161	H1-hESC	embryonic stem cell:	n/a	n/a
16	ATF3	chr3:158519568-158520077	A549	lung:	n/a	n/a
17	POLR2A	chr3:158519432-158520348	K562	blood:	n/a	n/a
18	POLR2A	chr3:158519489-158520115	A549	lung:	n/a	n/a
19	MAX	chr3:158518993-158520599	HepG2	liver:	n/a	chr3:158520438-158520447 chr3:158520436-158520446 chr3:158520189-158520198 chr3:158520435-158520450
20	POLR2A	chr3:158519430-158520129	PFSK-1	brain:	n/a	n/a
21	TAF1	chr3:158519381-158520163	ECC-1	luminal epithelium:	n/a	n/a
22	HCFC1	chr3:158519363-158520446	K562	blood:	n/a	n/a
23	ELK1	chr3:158519640-158520296	GM12878	blood:	n/a	n/a
24	ELF1	chr3:158519598-158520084	HepG2	liver:	n/a	n/a
25	ELF1	chr3:158519598-158520060	K562	blood:	n/a	n/a
26	POLR2A	chr3:158519048-158520423	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr3:158519310-158521018	HL-60	blood:	n/a	n/a
28	TAF1	chr3:158519592-158520378	GM12878	blood:	n/a	n/a
29	MAX	chr3:158519606-158520520	Hela-S3	cervix:	n/a	chr3:158520438-158520447 chr3:158520436-158520446 chr3:158520189-158520198 chr3:158520435-158520450
30	POLR2A	chr3:158519428-158520341	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr3:158518843-158520542	IMR90	lung:	n/a	n/a
32	NR2F2	chr3:158519337-158520658	K562	blood:	n/a	n/a
33	ATF3	chr3:158519433-158520028	K562	blood:	n/a	n/a
34	SIN3AK20	chr3:158519637-158520396	H1-hESC	embryonic stem cell:	n/a	n/a
35	USF1	chr3:158519291-158520378	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr3:158519257-158520430	MCF10A-Er-Src	breast:	n/a	n/a
37	NFIC	chr3:158519543-158520021	HepG2	liver:	n/a	n/a
38	EP300	chr3:158519646-158520024	SK-N-SH_RA	brain:	n/a	n/a
39	POLR2A	chr3:158519402-158520254	H1-neurons	neurons:	n/a	n/a
40	ATF3	chr3:158519634-158520014	HepG2	liver:	n/a	n/a
41	USF1	chr3:158519414-158520112	GM12878	blood:	n/a	n/a
42	SMARCC1	chr3:158519457-158520646	Hela-S3	cervix:	n/a	n/a
43	TBP	chr3:158519657-158520438	Hela-S3	cervix:	n/a	n/a
44	USF1	chr3:158519512-158520054	GM12878	blood:	n/a	n/a
45	E2F6	chr3:158519355-158520366	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr3:158519525-158520112	HEK293	kidney:	n/a	n/a
47	POLR2A	chr3:158519428-158520581	NB4	blood:	n/a	n/a
48	GABPA	chr3:158519546-158520080	A549	lung:	n/a	n/a
49	NFIC	chr3:158519550-158520159	ECC-1	luminal epithelium:	n/a	n/a
50	TCF7L2	chr3:158519435-158520099	HCT-116	colon:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:158519080..158523533-chr3:158523571..158529220,8	MCF-7	breast:
2	chr15:75660196..75660788-chr3:158519289..158520156,2	Hela-S3	cervix:
3	chr3:158519555..158521596-chr3:158521665..158523312,3	MCF-7	breast:

No data

Variant related genes	Relation type
MFSD1	TF binding region
ENSG00000272247	TF binding region
ENSG00000118855	Chromatin interaction
ENSG00000140400	Chromatin interaction
ENSG00000260274	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10513528	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936161	0.89[ASN][1000 genomes]
rs10936162	0.99[ASN][1000 genomes]
rs12490494	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12491877	0.99[EUR][1000 genomes]
rs12497958	0.90[ASN][1000 genomes]
rs1503099	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs41272621	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41434057	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs56857471	0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs61796768	0.99[EUR][1000 genomes]
rs61796770	0.99[EUR][1000 genomes]
rs61796775	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61796815	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61796817	0.85[AMR][1000 genomes]
rs6441226	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs73158361	0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1001450	chr3:158440011-158768399	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536777	chr3:158440011-158768399	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv877693	chr3:158470321-158583004	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv1006146	chr3:158475824-158625778	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv592123	chr3:158477796-158625128	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv1002514	chr3:158484027-158673414	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
14	nsv536778	chr3:158484027-158673414	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
15	nsv1014511	chr3:158516495-158715240	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer 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	12 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	chr3:158518600-158520200	Active TSS	Brain Anterior Caudate	brain
2	chr3:158518600-158520600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:158518600-158521400	Active TSS	Brain Cingulate Gyrus	brain
4	chr3:158518800-158520400	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr3:158518800-158520600	Active TSS	Fetal Heart	heart
6	chr3:158518800-158520600	Active TSS	Left Ventricle	heart
7	chr3:158518800-158520600	Active TSS	Pancreas	Pancrea
8	chr3:158518800-158520800	Active TSS	Colonic Mucosa	Colon
9	chr3:158518800-158520800	Active TSS	Fetal Intestine Large	intestine
10	chr3:158518800-158520800	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr3:158518800-158521200	Active TSS	Psoas Muscle	Psoas
12	chr3:158518800-158521400	Active TSS	Brain Hippocampus Middle	brain
13	chr3:158518800-158522000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:158519000-158520200	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr3:158519000-158520400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr3:158519000-158520400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:158519000-158520400	Active TSS	Lung	lung
18	chr3:158519000-158520400	Active TSS	Thymus	Thymus
19	chr3:158519000-158520600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:158519000-158520600	Active TSS	Esophagus	oesophagus
21	chr3:158519000-158520800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:158519000-158520800	Active TSS	Aorta	Aorta
23	chr3:158519000-158520800	Active TSS	Brain Angular Gyrus	brain
24	chr3:158519000-158520800	Active TSS	Ovary	ovary
25	chr3:158519000-158520800	Active TSS	A549	lung
26	chr3:158519000-158521000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:158519000-158521000	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr3:158519000-158521200	Active TSS	Brain Substantia Nigra	brain
29	chr3:158519000-158521400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:158519200-158520200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr3:158519200-158520200	Active TSS	Fetal Brain Female	brain
32	chr3:158519200-158520400	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr3:158519200-158520600	Active TSS	Colon Smooth Muscle	Colon
34	chr3:158519200-158520800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
35	chr3:158519200-158520800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:158519200-158520800	Active TSS	Fetal Stomach	stomach
37	chr3:158519200-158521000	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr3:158519200-158521000	Active TSS	Right Ventricle	heart
39	chr3:158519200-158521400	Active TSS	Rectal Smooth Muscle	rectum
40	chr3:158519200-158521600	Active TSS	Right Atrium	heart
41	chr3:158519400-158520200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:158519400-158520200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr3:158519400-158520200	Active TSS	Fetal Muscle Leg	muscle
44	chr3:158519400-158520200	Active TSS	Placenta Amnion	Placenta Amnion
45	chr3:158519400-158520200	Active TSS	Stomach Mucosa	stomach
46	chr3:158519400-158520200	Active TSS	Osteobl	bone
47	chr3:158519400-158520400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr3:158519400-158520400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:158519400-158520400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:158519400-158520400	Active TSS	Primary T cells from cord blood	blood

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