Variant report

Variant	rs28679552
Chromosome Location	chr2:54783603-54783604
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr2:54783601-54784119	GM12878	blood:	n/a	n/a
2	HEY1	chr2:54782308-54783686	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:54782355-54786484	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:54782394-54783807	HepG2	liver:	n/a	n/a
5	MXI1	chr2:54783574-54784218	GM12878	blood:	n/a	n/a
6	ARID3A	chr2:54783527-54783660	HepG2	liver:	n/a	chr2:54783540-54783556
7	POLR2A	chr2:54782528-54783621	HepG2	liver:	n/a	n/a
8	POLR2A	chr2:54783397-54783641	HepG2	liver:	n/a	n/a
9	RCOR1	chr2:54783398-54783641	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:54197301..54199396-chr2:54783418..54785695,2	MCF-7	breast:
2	chr2:54783297..54785333-chr2:54809031..54810704,2	K562	blood:
3	chr2:54772020..54776106-chr2:54782775..54785505,4	K562	blood:
4	chr2:54754602..54758699-chr2:54783105..54787010,4	MCF-7	breast:
5	chr2:54782515..54784267-chr2:54820223..54822640,2	MCF-7	breast:
6	chr2:54782460..54784855-chr2:54875341..54877678,2	K562	blood:

No data

Variant related genes	Relation type
SPTBN1	TF binding region
ENSG00000170634	Chromatin interaction
ENSG00000237887	Chromatin interaction
ENSG00000234943	Chromatin interaction
ENSG00000068878	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10169013	1.00[ASN][1000 genomes]
rs10171393	1.00[ASN][1000 genomes]
rs10172671	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10182310	1.00[ASN][1000 genomes]
rs10188548	1.00[ASN][1000 genomes]
rs10189084	1.00[ASN][1000 genomes]
rs10191357	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10194488	1.00[ASN][1000 genomes]
rs10195423	1.00[ASN][1000 genomes]
rs10206622	1.00[ASN][1000 genomes]
rs13391762	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13403817	1.00[ASN][1000 genomes]
rs13414727	1.00[ASN][1000 genomes]
rs13415413	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13415949	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13423872	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13425620	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13426037	1.00[ASN][1000 genomes]
rs13427468	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13428524	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431302	1.00[ASN][1000 genomes]
rs17045949	1.00[ASN][1000 genomes]
rs2229505	1.00[ASN][1000 genomes]
rs28496426	1.00[ASN][1000 genomes]
rs28609649	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28660202	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4387841	1.00[ASN][1000 genomes]
rs6545417	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545426	1.00[ASN][1000 genomes]
rs6735962	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6746379	1.00[ASN][1000 genomes]
rs7340250	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73934326	1.00[ASN][1000 genomes]
rs7574433	1.00[ASN][1000 genomes]
rs9808516	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv2731	chr2:54745069-54790057	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54768200-54783800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:54773400-54784000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:54773400-54784000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:54777600-54784800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:54777600-54784800	Weak transcription	Aorta	Aorta
6	chr2:54777800-54784200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:54778000-54784200	Weak transcription	Fetal Brain Male	brain
8	chr2:54778600-54784000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr2:54778800-54784000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:54778800-54784000	Weak transcription	Primary B cells from cord blood	blood
11	chr2:54779000-54784000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr2:54779200-54783800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr2:54779200-54784000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr2:54779200-54784000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr2:54779200-54784200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr2:54779400-54784200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr2:54779400-54784200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:54779800-54784200	Enhancers	NHDF-Ad	bronchial
19	chr2:54779800-54784600	Enhancers	Right Ventricle	heart
20	chr2:54780200-54783800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr2:54780800-54784400	Enhancers	Primary T cells from cord blood	blood
22	chr2:54781000-54784600	Enhancers	Fetal Intestine Small	intestine
23	chr2:54781000-54784800	Enhancers	Right Atrium	heart
24	chr2:54781200-54784200	Weak transcription	K562	blood
25	chr2:54781200-54784600	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr2:54781400-54783800	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr2:54781400-54784400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:54781400-54784400	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr2:54781400-54784800	Enhancers	Left Ventricle	heart
30	chr2:54781600-54784000	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr2:54781600-54784000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr2:54781600-54784200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:54781800-54784600	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr2:54781800-54784600	Enhancers	Adipose Nuclei	Adipose
35	chr2:54781800-54784600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr2:54781800-54784600	Enhancers	Fetal Intestine Large	intestine
37	chr2:54781800-54784800	Enhancers	Brain Anterior Caudate	brain
38	chr2:54782000-54784200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:54782000-54784400	Enhancers	Colon Smooth Muscle	Colon
40	chr2:54782000-54784800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:54782000-54784800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr2:54782000-54784800	Weak transcription	Psoas Muscle	Psoas
43	chr2:54782200-54784400	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr2:54782200-54784600	Enhancers	HMEC	breast
45	chr2:54782200-54784600	Enhancers	HUVEC	blood vessel
46	chr2:54782200-54784800	Enhancers	Pancreas	Pancrea
47	chr2:54782200-54785600	Enhancers	Fetal Heart	heart
48	chr2:54782400-54784000	Enhancers	Osteobl	bone
49	chr2:54782400-54784200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:54782400-54784200	Enhancers	GM12878-XiMat	blood

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