Variant report

Variant	rs56149931
Chromosome Location	chr2:39354512-39354513
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	POLR2A	chr2:39354333-39354753	SK-N-MC	brain:	n/a	n/a
2	CEBPB	chr2:39354220-39354564	Hela-S3	cervix:	n/a	n/a
3	STAT3	chr2:39354293-39354573	MCF10A-Er-Src	breast:	n/a	n/a
4	CEBPB	chr2:39354269-39354563	IMR90	lung:	n/a	n/a
5	STAT3	chr2:39354337-39354600	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr2:39354296-39354612	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39350652..39354915-chr2:39355009..39358498,5	K562	blood:
2	chr2:39351946..39354916-chr2:39358761..39361361,2	K562	blood:

Variant related genes	Relation type
SOS1	TF binding region
ENSG00000202309	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11896463	1.00[AMR][1000 genomes]
rs13428418	1.00[ASN][1000 genomes]
rs56065106	1.00[AMR][1000 genomes]
rs59983786	1.00[AMR][1000 genomes]
rs73930376	1.00[AMR][1000 genomes]
rs73930385	1.00[AMR][1000 genomes]
rs73930386	1.00[AMR][1000 genomes]
rs73930394	1.00[AMR][1000 genomes]
rs73930512	1.00[AMR][1000 genomes]
rs73934118	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755359	chr2:39169049-39417849	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1010874	chr2:39255376-39604535	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv535649	chr2:39255376-39604535	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats 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	35 gene(s)	inside rSNPs	diseases
5	nsv531346	chr2:39263225-39606367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv533348	chr2:39264345-39596169	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv1014520	chr2:39270598-39596299	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv535650	chr2:39270598-39596299	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	nsv1008198	chr2:39271472-39364035	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
10	nsv1009379	chr2:39271472-39604535	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
11	nsv581493	chr2:39277851-39547575	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
12	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
13	nsv533456	chr2:39281834-39596298	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
14	nsv581495	chr2:39282079-39475205	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39352400-39355000	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr2:39352400-39355000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:39352400-39355200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:39352400-39356800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr2:39352600-39354600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr2:39352600-39355000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:39352600-39355200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:39352600-39355200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:39352600-39355200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr2:39352600-39355200	Weak transcription	Fetal Lung	lung
11	chr2:39352600-39355200	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:39352600-39355200	Weak transcription	Fetal Thymus	thymus
13	chr2:39352600-39355600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:39352600-39356400	Weak transcription	Small Intestine	intestine
15	chr2:39352600-39356600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr2:39352800-39354600	Weak transcription	GM12878-XiMat	blood
17	chr2:39352800-39354800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:39352800-39355000	Weak transcription	Primary B cells from cord blood	blood
19	chr2:39352800-39355000	Weak transcription	Primary B cells from peripheral blood	blood
20	chr2:39352800-39355000	Weak transcription	Primary T cells from cord blood	blood
21	chr2:39352800-39355000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr2:39352800-39355000	Weak transcription	A549	lung
23	chr2:39352800-39355000	Weak transcription	NHEK	skin
24	chr2:39352800-39355200	Weak transcription	Fetal Intestine Large	intestine
25	chr2:39352800-39362800	Weak transcription	Thymus	Thymus
26	chr2:39352800-39368600	Weak transcription	HMEC	breast
27	chr2:39353000-39354600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:39353000-39354600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr2:39353000-39354600	Weak transcription	Adipose Nuclei	Adipose
30	chr2:39353000-39355000	Weak transcription	Dnd41	blood
31	chr2:39353000-39355200	Weak transcription	Brain Anterior Caudate	brain
32	chr2:39353000-39355200	Weak transcription	Fetal Intestine Small	intestine
33	chr2:39353000-39355200	Weak transcription	HepG2	liver
34	chr2:39353800-39355400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr2:39354200-39354600	Active TSS	Aorta	Aorta
36	chr2:39354200-39354600	Active TSS	Osteobl	bone
37	chr2:39354200-39355000	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr2:39354200-39355400	Enhancers	Hela-S3	cervix
39	chr2:39354200-39356600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:39354200-39357800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:39354200-39358400	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr2:39354400-39354600	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr2:39354400-39354600	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr2:39354400-39354600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:39354400-39354600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:39354400-39354600	Enhancers	K562	blood
47	chr2:39354400-39354600	Flanking Active TSS	NHDF-Ad	bronchial
48	chr2:39354400-39354800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:39354400-39354800	Active TSS	Primary monocytes fromperipheralblood	blood
50	chr2:39354400-39354800	Active TSS	NHLF	lung

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