Variant report

Variant	rs6725834
Chromosome Location	chr2:48754898-48754899
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	TCF12	chr2:48754320-48754928	SK-N-SH	brain:	n/a	n/a
2	PBX3	chr2:48754400-48755053	SK-N-SH	brain:	n/a	n/a
3	PBX3	chr2:48754331-48755155	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr2:48754348-48754915	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48752578..48754982-chr2:48756156..48759647,3	K562	blood:
2	chr2:48752578..48754982-chr2:48756701..48759647,2	K562	blood:

Variant related genes	Relation type
STON1-GTF2A1L	TF binding region
STON1	TF binding region
ENSG00000243244	Chromatin interaction
ENSG00000068781	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1404057	1.00[CHD][hapmap]
rs1464728	1.00[CHD][hapmap]
rs1524149	1.00[CHD][hapmap]
rs1554613	1.00[CHD][hapmap]
rs4953611	1.00[CHD][hapmap]
rs4953617	1.00[CHD][hapmap]
rs6545031	1.00[CHD][hapmap]
rs6545049	1.00[AMR][1000 genomes]
rs6712571	1.00[CHD][hapmap]
rs6717383	0.88[EUR][1000 genomes]
rs7563625	1.00[CHD][hapmap]
rs7578522	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005954	chr2:48692696-48905723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv535682	chr2:48692696-48905723	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv833981	chr2:48705444-48878179	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1007491	chr2:48752185-48796441	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv535683	chr2:48752185-48796441	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48709400-48755200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:48726400-48756800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:48728200-48756800	Weak transcription	HMEC	breast
4	chr2:48737800-48756200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:48738000-48755400	Weak transcription	HUVEC	blood vessel
6	chr2:48738000-48756800	Weak transcription	NH-A	brain
7	chr2:48740000-48756000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:48740000-48757600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:48742400-48756200	Weak transcription	NHDF-Ad	bronchial
10	chr2:48743200-48756000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr2:48743200-48756200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:48743200-48756800	Weak transcription	Stomach Mucosa	stomach
13	chr2:48743400-48756200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr2:48743400-48756400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr2:48743400-48757400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:48743400-48757400	Weak transcription	Gastric	stomach
17	chr2:48744000-48756600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:48744000-48756800	Weak transcription	Colonic Mucosa	Colon
19	chr2:48744600-48756400	Weak transcription	Brain Germinal Matrix	brain
20	chr2:48744800-48755800	Weak transcription	HepG2	liver
21	chr2:48744800-48756200	Weak transcription	Fetal Brain Female	brain
22	chr2:48745200-48756200	Weak transcription	Esophagus	oesophagus
23	chr2:48745600-48755200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr2:48745600-48756800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr2:48745800-48756400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr2:48745800-48756400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr2:48745800-48756400	Weak transcription	Brain Angular Gyrus	brain
28	chr2:48745800-48756400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr2:48746000-48755200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:48746000-48756400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr2:48746000-48756400	Weak transcription	A549	lung
32	chr2:48746000-48756400	Weak transcription	HSMM	muscle
33	chr2:48746400-48756400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:48746800-48756600	Weak transcription	Osteobl	bone
35	chr2:48746800-48756800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:48747000-48755000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr2:48747000-48756000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr2:48747000-48756800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:48747000-48756800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:48748200-48756400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr2:48748200-48756400	Weak transcription	GM12878-XiMat	blood
42	chr2:48748200-48756800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:48748200-48756800	Weak transcription	NHEK	skin
44	chr2:48748400-48756000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr2:48748600-48756200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr2:48748600-48756400	Weak transcription	Dnd41	blood
47	chr2:48748800-48756400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr2:48749000-48755200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr2:48749400-48755400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr2:48749400-48755800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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