Variant report

Variant	rs58342359
Chromosome Location	chr4:2813297-2813298
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	MTA3	chr4:2813221-2816423	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:2813291-2814441	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr4:2813221-2814866	GM12878	blood:	n/a	n/a
4	TCF12	chr4:2813251-2814371	ECC-1	luminal epithelium:	n/a	chr4:2813598-2813608
5	POLR2A	chr4:2811919-2815260	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:2812096..2814174-chr4:2819979..2821555,2	MCF-7	breast:
2	chr4:2812607..2814330-chr4:2927336..2930211,2	MCF-7	breast:
3	chr4:2811128..2813446-chr4:2813847..2818794,5	MCF-7	breast:
4	chr4:2811854..2813390-chr4:2936367..2938521,2	MCF-7	breast:

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

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11934244	0.89[ASN][1000 genomes]
rs16843167	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843419	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59360049	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62620003	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73082303	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs743694	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2796200-2813800	Enhancers	Left Ventricle	heart
2	chr4:2796600-2814600	Enhancers	Stomach Mucosa	stomach
3	chr4:2803200-2813400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:2803400-2819200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:2803600-2813400	Enhancers	Primary B cells from cord blood	blood
6	chr4:2804600-2813800	Genic enhancers	Placenta	Placenta
7	chr4:2806000-2814600	Enhancers	Liver	Liver
8	chr4:2808000-2813400	Enhancers	Adipose Nuclei	Adipose
9	chr4:2808400-2813800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:2809000-2813400	Weak transcription	NH-A	brain
11	chr4:2809000-2813400	Weak transcription	Osteobl	bone
12	chr4:2809200-2813400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:2809200-2813400	Weak transcription	Fetal Kidney	kidney
14	chr4:2809200-2815200	Weak transcription	Fetal Brain Female	brain
15	chr4:2809400-2813400	Weak transcription	Fetal Brain Male	brain
16	chr4:2809400-2813400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr4:2810000-2813600	Enhancers	Primary B cells from peripheral blood	blood
18	chr4:2811000-2813400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr4:2811000-2813600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:2811000-2813600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr4:2811000-2813600	Enhancers	Fetal Muscle Trunk	muscle
22	chr4:2811000-2813600	Enhancers	Lung	lung
23	chr4:2811000-2815200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:2811000-2816000	Enhancers	Brain Substantia Nigra	brain
25	chr4:2811200-2813400	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr4:2811200-2813400	Genic enhancers	Fetal Stomach	stomach
27	chr4:2811200-2813400	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr4:2811200-2813600	Enhancers	Primary hematopoietic stem cells	blood
29	chr4:2811200-2813600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr4:2811200-2813800	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr4:2811200-2814000	Enhancers	Fetal Intestine Large	intestine
32	chr4:2811200-2814200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:2811200-2814600	Enhancers	Brain Anterior Caudate	brain
34	chr4:2811200-2814600	Genic enhancers	Fetal Intestine Small	intestine
35	chr4:2811200-2815000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr4:2811400-2814800	Enhancers	H1 Cell Line	embryonic stem cell
37	chr4:2811600-2813400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr4:2811600-2813400	Weak transcription	Fetal Lung	lung
39	chr4:2811600-2813600	Enhancers	Brain Hippocampus Middle	brain
40	chr4:2811600-2815400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:2811800-2813400	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr4:2811800-2813400	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr4:2811800-2813600	Enhancers	Fetal Muscle Leg	muscle
44	chr4:2811800-2813800	Enhancers	Spleen	Spleen
45	chr4:2811800-2814400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:2811800-2815200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr4:2811800-2819400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr4:2812000-2813400	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr4:2812000-2813400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr4:2812000-2813400	Weak transcription	Colon Smooth Muscle	Colon

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