Variant report

Variant	rs172998
Chromosome Location	chr4:2800529-2800530
allele	A/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	MAZ	chr4:2799993-2801038	GM12878	blood:	n/a	n/a
2	YY1	chr4:2800113-2800891	GM12878	blood:	n/a	n/a
3	POLR2A	chr4:2799336-2801572	HL-60	blood:	n/a	n/a
4	TFAP2C	chr4:2799856-2801210	Hela-S3	cervix:	n/a	chr4:2800624-2800633 chr4:2800501-2800516
5	ATF2	chr4:2800024-2800854	GM12878	blood:	n/a	n/a
6	RELA	chr4:2800040-2800903	GM18951	blood:	n/a	n/a
7	RFX5	chr4:2800398-2800754	Hela-S3	cervix:	n/a	n/a
8	GATA3	chr4:2800187-2801037	MCF-7	breast:	n/a	n/a
9	GATA3	chr4:2800180-2800584	SH-SY5Y	brain:	n/a	n/a
10	USF2	chr4:2800469-2800714	Hela-S3	cervix:	n/a	chr4:2800673-2800689
11	NRF1	chr4:2800470-2800617	GM12878	blood:	n/a	n/a
12	MTA3	chr4:2799765-2801438	GM12878	blood:	n/a	n/a
13	SMC3	chr4:2800454-2800785	Hela-S3	cervix:	n/a	n/a
14	REST	chr4:2800105-2800555	SK-N-SH	brain:	n/a	chr4:2800337-2800350 chr4:2800141-2800154 chr4:2800398-2800416
15	SPI1	chr4:2800015-2800761	GM12878	blood:	n/a	chr4:2800277-2800284 chr4:2800480-2800489 chr4:2800620-2800633
16	RELA	chr4:2800179-2800846	GM19193	blood:	n/a	n/a
17	EP300	chr4:2800128-2800650	GM12878	blood:	n/a	n/a
18	EP300	chr4:2799226-2800968	SK-N-SH	brain:	n/a	chr4:2800672-2800688 chr4:2800675-2800691
19	CHD2	chr4:2800344-2800839	Hela-S3	cervix:	n/a	chr4:2800681-2800691
20	ZNF143	chr4:2800498-2800781	Hela-S3	cervix:	n/a	n/a
21	EBF1	chr4:2799391-2800909	GM12878	blood:	n/a	chr4:2800635-2800646
22	POLR2A	chr4:2799845-2800959	GM18951	blood:	n/a	n/a
23	FOXP2	chr4:2800125-2800772	PFSK-1	brain:	n/a	n/a
24	POLR2A	chr4:2800113-2800877	PANC-1	pancreas:	n/a	n/a
25	EP300	chr4:2800229-2800640	GM12878	blood:	n/a	n/a
26	TCF12	chr4:2800439-2800749	GM12878	blood:	n/a	n/a
27	TBL1XR1	chr4:2800111-2800901	GM12878	blood:	n/a	n/a
28	POLR2A	chr4:2800166-2800941	GM12892	blood:	n/a	n/a
29	POLR2A	chr4:2800363-2800947	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr4:2799733-2801394	GM19193	blood:	n/a	n/a
31	ELK1	chr4:2800462-2800730	Hela-S3	cervix:	n/a	n/a
32	MAZ	chr4:2800482-2800870	Hela-S3	cervix:	n/a	n/a
33	ELF1	chr4:2800323-2800863	MCF-7	breast:	n/a	n/a
34	TCF7L2	chr4:2800444-2800814	PANC-1	pancreas:	n/a	n/a
35	MAX	chr4:2800235-2800996	GM12878	blood:	n/a	n/a
36	POLR2A	chr4:2800059-2801070	GM12878	blood:	n/a	n/a
37	USF2	chr4:2800159-2800692	GM12878	blood:	n/a	chr4:2800673-2800689
38	STAT1	chr4:2800068-2800780	GM12878	blood:	n/a	chr4:2800654-2800666 chr4:2800621-2800633 chr4:2800258-2800270 chr4:2800611-2800623 chr4:2800681-2800693
39	RUNX3	chr4:2799926-2800898	GM12878	blood:	n/a	n/a
40	ELF1	chr4:2799640-2801633	GM12878	blood:	n/a	n/a
41	CEBPB	chr4:2800491-2800804	Hela-S3	cervix:	n/a	n/a
42	BHLHE40	chr4:2800129-2800807	GM12878	blood:	n/a	chr4:2800673-2800689
43	MXI1	chr4:2800040-2800859	GM12878	blood:	n/a	n/a
44	GATA2	chr4:2799499-2800695	SH-SY5Y	brain:	n/a	n/a
45	SMARCC1	chr4:2800095-2801140	Hela-S3	cervix:	n/a	n/a
46	EBF1	chr4:2800102-2800769	GM12878	blood:	n/a	chr4:2800635-2800646
47	GTF2F1	chr4:2800376-2800733	Hela-S3	cervix:	n/a	n/a
48	MAX	chr4:2800128-2800767	NB4	blood:	n/a	n/a
49	RUNX3	chr4:2799977-2801396	GM12878	blood:	n/a	n/a
50	MAX	chr4:2800274-2800801	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:2794084..2803742-chr4:2816227..2824357,23	MCF-7	breast:
2	chr4:2795447..2803617-chr4:2934606..2939244,18	MCF-7	breast:
3	chr4:2799331..2801814-chr4:2936733..2939693,2	K562	blood:
4	chr4:2790052..2809152-chr4:2930639..2948075,83	MCF-7	breast:
5	chr4:2794525..2804465-chr4:2841103..2847851,19	MCF-7	breast:
6	chr4:2798106..2801583-chr4:2843513..2845994,4	MCF-7	breast:
7	chr4:2798213..2801828-chr4:2930948..2933812,4	MCF-7	breast:
8	chr4:2754950..2759334-chr4:2798371..2803453,5	MCF-7	breast:
9	chr4:2798770..2801758-chr4:2941180..2943976,2	K562	blood:
10	chr4:2753714..2768807-chr4:2789818..2806638,47	MCF-7	breast:
11	chr4:2793845..2803067-chr4:2816443..2823671,22	MCF-7	breast:

Variant related genes	Relation type
SH3BP2	TF binding region
ENSG00000249673	Chromatin interaction
ENSG00000087274	Chromatin interaction
ENSG00000168884	Chromatin interaction
ENSG00000087266	Chromatin interaction
ENSG00000087269	Chromatin interaction
ENSG00000109736	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1263449	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1271256	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1751848	0.85[CEU][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs182820	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs190160	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs231334	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs231339	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs381101	0.82[ASN][1000 genomes]
rs382379	0.86[CEU][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs390288	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs392479	0.83[ASN][1000 genomes]
rs397292	0.82[ASN][1000 genomes]
rs402855	0.83[ASN][1000 genomes]
rs407770	0.82[ASN][1000 genomes]
rs408102	0.94[ASN][1000 genomes]
rs419096	0.82[ASN][1000 genomes]
rs438524	0.83[ASN][1000 genomes]
rs743691	0.89[CEU][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs762833	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs762834	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7677047	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948659	chr4:1828867-2815632	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv1005116	chr4:2633935-2812340	Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv878444	chr4:2689449-2861090	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv470002	chr4:2701098-2836628	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv878445	chr4:2704046-2831383	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv878446	chr4:2710644-2810634	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv878447	chr4:2723531-2831383	Flanking Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv516797	chr4:2723531-2836628	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv878448	chr4:2723531-2846799	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
11	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	63 gene(s)	inside rSNPs	diseases
12	nsv878449	chr4:2744480-2831383	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription 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	19 gene(s)	inside rSNPs	diseases
13	nsv1002517	chr4:2747905-2822017	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Strong transcription 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	19 gene(s)	inside rSNPs	diseases
14	nsv878450	chr4:2760222-2861090	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
15	nsv967941	chr4:2765555-2802771	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv593435	chr4:2770772-2881256	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
17	nsv878451	chr4:2785556-2856687	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
18	nsv878452	chr4:2789184-2830076	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
19	nsv1010533	chr4:2792848-2873441	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
20	nsv461162	chr4:2794320-2846799	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
21	nsv593436	chr4:2794320-2846799	Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
22	esv3374181	chr4:2799604-2802102	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2795400-2801400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:2795800-2803000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:2796000-2802400	Enhancers	Brain Germinal Matrix	brain
4	chr4:2796000-2803400	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr4:2796000-2803600	Enhancers	Fetal Brain Male	brain
6	chr4:2796000-2803800	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr4:2796200-2802000	Enhancers	Fetal Muscle Trunk	muscle
8	chr4:2796200-2802400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:2796200-2803400	Enhancers	Pancreas	Pancrea
10	chr4:2796200-2803400	Enhancers	Right Atrium	heart
11	chr4:2796200-2803600	Enhancers	Fetal Brain Female	brain
12	chr4:2796200-2813800	Enhancers	Left Ventricle	heart
13	chr4:2796400-2800600	Enhancers	Gastric	stomach
14	chr4:2796600-2803600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:2796600-2814600	Enhancers	Stomach Mucosa	stomach
16	chr4:2796800-2801200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:2796800-2802200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr4:2796800-2803600	Enhancers	NHDF-Ad	bronchial
19	chr4:2796800-2803800	Enhancers	HUVEC	blood vessel
20	chr4:2797000-2801200	Enhancers	Fetal Thymus	thymus
21	chr4:2797000-2802000	Weak transcription	Ovary	ovary
22	chr4:2797000-2803800	Enhancers	Muscle Satellite Cultured Cells	--
23	chr4:2797200-2800800	Weak transcription	Psoas Muscle	Psoas
24	chr4:2797200-2801200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:2797400-2801600	Enhancers	Fetal Intestine Large	intestine
26	chr4:2797400-2802200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr4:2797400-2802400	Enhancers	Brain Cingulate Gyrus	brain
28	chr4:2797800-2802400	Enhancers	Brain Substantia Nigra	brain
29	chr4:2798000-2800600	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr4:2798000-2800800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr4:2798000-2801200	Enhancers	HSMM	muscle
32	chr4:2798000-2803800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:2798200-2801400	Enhancers	Colon Smooth Muscle	Colon
34	chr4:2798200-2803400	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr4:2798400-2800600	Enhancers	HSMMtube	muscle
36	chr4:2798400-2800800	Enhancers	Brain Angular Gyrus	brain
37	chr4:2798400-2801400	Flanking Active TSS	Stomach Smooth Muscle	stomach
38	chr4:2798400-2809600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr4:2798600-2800600	Genic enhancers	Placenta	Placenta
40	chr4:2798600-2801800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:2798600-2803800	Enhancers	Fetal Lung	lung
42	chr4:2798800-2800600	Genic enhancers	NHLF	lung
43	chr4:2798800-2801600	Enhancers	HepG2	liver
44	chr4:2798800-2801800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr4:2798800-2801800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:2798800-2802200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr4:2798800-2802400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr4:2798800-2803400	Enhancers	NHEK	skin
49	chr4:2799000-2801400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr4:2799000-2801600	Enhancers	Right Ventricle	heart

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