Variant report

Variant	rs2282771
Chromosome Location	chr4:2830215-2830216
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:2830059-2830451	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:2830210-2830323	HepG2	liver:	n/a	n/a
3	POLR2A	chr4:2830106-2830720	HL-60	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:2793270..2794844-chr4:2830129..2831853,2	MCF-7	breast:
2	chr4:2826806..2829298-chr4:2829987..2832015,2	MCF-7	breast:
3	chr4:2824960..2827685-chr4:2829062..2834190,6	MCF-7	breast:
4	chr4:2824402..2830718-chr4:2842859..2847645,11	MCF-7	breast:
5	chr4:2794178..2796870-chr4:2828744..2832985,4	MCF-7	breast:
6	chr4:2825128..2826717-chr4:2829308..2831274,2	MCF-7	breast:

No data

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

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs13113803	0.95[CHB][hapmap]
rs13137906	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1784148	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs1784149	0.96[CHB][hapmap];0.84[ASN][1000 genomes]
rs2269484	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2269485	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213501	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34993433	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs370470	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs382379	0.80[CHB][hapmap]
rs385715	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs393635	0.80[ASN][1000 genomes]
rs397292	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs402855	0.83[ASN][1000 genomes]
rs407770	0.83[ASN][1000 genomes]
rs419096	0.83[ASN][1000 genomes]
rs421714	0.89[ASN][1000 genomes]
rs422734	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs426904	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs433030	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs445160	0.90[ASN][1000 genomes]
rs450080	0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6820967	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs743691	0.88[CHB][hapmap]
rs9685721	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	esv3440097	chr4:2827054-2831752	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2820600-2832400	Weak transcription	NHDF-Ad	bronchial
2	chr4:2820600-2839000	Weak transcription	Right Atrium	heart
3	chr4:2820600-2839200	Weak transcription	Brain Angular Gyrus	brain
4	chr4:2820600-2844600	Weak transcription	Psoas Muscle	Psoas
5	chr4:2820800-2835200	Weak transcription	HUVEC	blood vessel
6	chr4:2820800-2835400	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr4:2820800-2839600	Weak transcription	NHEK	skin
8	chr4:2821000-2844400	Weak transcription	HMEC	breast
9	chr4:2821200-2831400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:2821200-2834200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr4:2821200-2835400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr4:2821400-2836200	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr4:2821400-2837800	Weak transcription	Small Intestine	intestine
14	chr4:2821600-2835400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr4:2821800-2835800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr4:2821800-2835800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:2821800-2838000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:2821800-2838000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr4:2821800-2838200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:2821800-2838600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:2821800-2838800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:2821800-2844200	Weak transcription	Hela-S3	cervix
23	chr4:2822000-2831600	Weak transcription	NH-A	brain
24	chr4:2822000-2833600	Strong transcription	Primary B cells from cord blood	blood
25	chr4:2822000-2835200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr4:2822000-2835600	Strong transcription	Colonic Mucosa	Colon
27	chr4:2822000-2836000	Strong transcription	Primary T cells from cord blood	blood
28	chr4:2822000-2837200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr4:2822000-2837600	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr4:2822200-2836400	Strong transcription	Thymus	Thymus
31	chr4:2822200-2837600	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr4:2822400-2835800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr4:2822400-2838200	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr4:2822600-2833400	Strong transcription	Primary B cells from peripheral blood	blood
35	chr4:2822600-2835800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr4:2822600-2835800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr4:2822600-2835800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr4:2822600-2836200	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr4:2822600-2836600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr4:2822600-2836600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr4:2822600-2836800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:2822600-2836800	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr4:2822600-2838200	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr4:2822600-2838400	Strong transcription	Lung	lung
45	chr4:2822800-2838000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr4:2823200-2835000	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr4:2823800-2837000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr4:2823800-2837200	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr4:2823800-2837400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr4:2824000-2837200	Strong transcription	Rectal Mucosa Donor 31	rectum

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