Variant report

Variant	rs55946257
Chromosome Location	chr1:114415798-114415799
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:114415752-114416380	MCF-7	breast:	n/a	chr1:114416278-114416299

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114396190..114400486-chr1:114415320..114417523,4	MCF-7	breast:
2	chr1:114410354..114414312-chr1:114415133..114418521,4	K562	blood:
3	chr1:114415714..114417766-chr1:114443155..114445655,2	MCF-7	breast:
4	chr1:114415189..114417454-chr1:114422016..114424443,3	MCF-7	breast:
5	chr1:114414869..114417107-chr1:114504505..114506376,2	MCF-7	breast:
6	chr1:114406415..114409369-chr1:114414914..114416581,3	K562	blood:
7	chr1:114414556..114418668-chr1:114471915..114474547,3	K562	blood:
8	chr1:114415525..114417374-chr1:114419070..114421891,2	K562	blood:
9	chr1:114403069..114405298-chr1:114414916..114416570,2	MCF-7	breast:
10	chr1:114406159..114409369-chr1:114414864..114416515,3	K562	blood:
11	chr1:114414414..114416585-chr1:114444953..114447889,2	K562	blood:
12	chr1:114415510..114417903-chr1:114447530..114449794,2	MCF-7	breast:

No data

Variant related genes	Relation type
PTPN22	TF binding region
ENSG00000134262	Chromatin interaction
ENSG00000118655	Chromatin interaction
ENSG00000235527	Chromatin interaction
ENSG00000163349	Chromatin interaction
ENSG00000134242	Chromatin interaction
ENSG00000226167	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11102679	1.00[ASN][1000 genomes]
rs11102680	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12060671	1.00[AMR][1000 genomes]
rs12063602	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12064048	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12072840	1.00[AMR][1000 genomes]
rs12086911	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12090627	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12094849	1.00[ASN][1000 genomes]
rs12095398	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12097198	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34639107	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs998315	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114410000-114417800	Enhancers	NHEK	skin
2	chr1:114412600-114416000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr1:114412600-114417600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:114414000-114415800	Enhancers	Adipose Nuclei	Adipose
5	chr1:114414200-114417600	Enhancers	HUVEC	blood vessel
6	chr1:114414400-114415800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
7	chr1:114414400-114415800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:114414400-114415800	Flanking Active TSS	GM12878-XiMat	blood
9	chr1:114414400-114417200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:114415000-114447000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:114415200-114416600	Weak transcription	NH-A	brain
12	chr1:114415200-114418200	Enhancers	Primary hematopoietic stem cells	blood
13	chr1:114415200-114418600	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr1:114415400-114416600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr1:114415400-114416800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:114415400-114417400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:114415400-114417600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:114415400-114417800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:114415400-114419000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr1:114415400-114428800	Weak transcription	Colonic Mucosa	Colon
21	chr1:114415400-114437000	Weak transcription	Thymus	Thymus
22	chr1:114415600-114416000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:114415600-114416000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr1:114415600-114416600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:114415600-114416600	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr1:114415600-114416600	Weak transcription	Primary B cells from peripheral blood	blood
27	chr1:114415600-114416600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:114415600-114416600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:114415600-114416600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:114415600-114416600	Weak transcription	HMEC	breast
31	chr1:114415600-114416600	Weak transcription	K562	blood
32	chr1:114415600-114416800	Weak transcription	Fetal Thymus	thymus
33	chr1:114415600-114416800	Weak transcription	Small Intestine	intestine
34	chr1:114415600-114417000	Weak transcription	Osteobl	bone
35	chr1:114415600-114417200	Enhancers	Primary B cells from cord blood	blood
36	chr1:114415600-114417200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:114415600-114417400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr1:114415600-114417400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr1:114415600-114417400	Enhancers	Dnd41	blood
40	chr1:114415600-114417600	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr1:114415600-114417600	Enhancers	Primary T cells from cord blood	blood
42	chr1:114415600-114417800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:114415600-114417800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:114415600-114418000	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr1:114415600-114418200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr1:114415600-114418400	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr1:114415600-114418800	Enhancers	Primary T helper cells PMA-I stimulated	--

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