Variant report

Variant	rs231339
Chromosome Location	chr4:2809120-2809121
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	MXI1	chr4:2807983-2809253	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:2805467..2811002-chr4:2816486..2823721,11	MCF-7	breast:
2	chr4:2790052..2809152-chr4:2930639..2948075,83	MCF-7	breast:
3	chr4:2806060..2809541-chr4:2819791..2822068,4	MCF-7	breast:
4	chr4:2807216..2810880-chr4:2811664..2814785,3	MCF-7	breast:

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

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1263449	0.81[AMR][1000 genomes]
rs1271256	0.81[AMR][1000 genomes]
rs1626813	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs172998	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1751848	0.99[ASN][1000 genomes]
rs182820	0.80[ASN][1000 genomes]
rs189139	0.80[AFR][1000 genomes]
rs190160	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs231334	0.83[ASN][1000 genomes]
rs231396	0.80[AFR][1000 genomes]
rs231402	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs365569	0.86[ASN][1000 genomes]
rs381101	0.97[ASN][1000 genomes]
rs382379	0.99[ASN][1000 genomes]
rs392479	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs408102	0.80[ASN][1000 genomes]
rs438524	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7677047	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][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	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	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
16	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
17	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
18	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
19	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
20	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:98 , 50 per page) page: 1 2

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	chr4:2798400-2809600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:2801800-2809800	Enhancers	Fetal Intestine Large	intestine
5	chr4:2802800-2810200	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr4:2803000-2810600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:2803200-2811600	Enhancers	Right Ventricle	heart
8	chr4:2803200-2813400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:2803400-2811600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:2803400-2812800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr4:2803400-2819200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr4:2803600-2812600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr4:2803600-2813000	Weak transcription	Primary T cells from cord blood	blood
14	chr4:2803600-2813200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:2803600-2813400	Enhancers	Primary B cells from cord blood	blood
16	chr4:2803800-2813000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr4:2804200-2811400	Weak transcription	HepG2	liver
18	chr4:2804400-2811800	Genic enhancers	Primary monocytes fromperipheralblood	blood
19	chr4:2804400-2811800	Genic enhancers	Spleen	Spleen
20	chr4:2804600-2809400	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr4:2804600-2810000	Enhancers	Lung	lung
22	chr4:2804600-2813800	Genic enhancers	Placenta	Placenta
23	chr4:2804800-2809600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:2805200-2809600	Genic enhancers	Fetal Intestine Small	intestine
25	chr4:2805800-2809400	Enhancers	Fetal Brain Male	brain
26	chr4:2805800-2810000	Enhancers	Fetal Muscle Trunk	muscle
27	chr4:2805800-2812400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr4:2806000-2814600	Enhancers	Liver	Liver
29	chr4:2806400-2809400	Enhancers	Brain Substantia Nigra	brain
30	chr4:2806400-2809600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr4:2806400-2809600	Enhancers	Fetal Heart	heart
32	chr4:2806400-2810000	Enhancers	Gastric	stomach
33	chr4:2806600-2809400	Enhancers	Small Intestine	intestine
34	chr4:2806600-2809600	Enhancers	Fetal Lung	lung
35	chr4:2806600-2809600	Enhancers	Right Atrium	heart
36	chr4:2806600-2809800	Enhancers	Pancreas	Pancrea
37	chr4:2806600-2810400	Enhancers	Brain Anterior Caudate	brain
38	chr4:2807000-2809200	Enhancers	Fetal Brain Female	brain
39	chr4:2807000-2809200	Enhancers	HUVEC	blood vessel
40	chr4:2807000-2810200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr4:2807200-2809200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:2807200-2809400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:2807200-2809400	Enhancers	NHDF-Ad	bronchial
44	chr4:2807200-2809600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr4:2807200-2809600	Enhancers	Ovary	ovary
46	chr4:2807600-2809200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr4:2807600-2809600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr4:2807600-2809600	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr4:2807600-2809800	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr4:2807600-2810600	Enhancers	Brain Germinal Matrix	brain

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