Variant report

Variant	rs6548005
Chromosome Location	chr2:30480196-30480197
allele	C/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	GATA2	chr2:30479816-30480325	SH-SY5Y	brain:	n/a	chr2:30479994-30480003
2	MXI1	chr2:30480071-30480201	K562	blood:	n/a	n/a
3	POLR2A	chr2:30479645-30484280	A549	lung:	n/a	n/a
4	POLR2A	chr2:30477119-30482747	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:30451092..30457677-chr2:30474497..30480716,15	K562	blood:
2	chr2:30475438..30481096-chr2:30481124..30485591,9	K562	blood:
3	chr2:30475603..30478549-chr2:30478723..30480577,2	K562	blood:
4	chr2:30475984..30481096-chr2:30481124..30486276,10	K562	blood:

Variant related genes	Relation type
ENSG00000256261	TF binding region
ENSG00000213626	Chromatin interaction
ENSG00000256261	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1001204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10171296	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs10171305	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11676884	0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs13386455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13389106	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17009304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17009315	0.91[CEU][hapmap]
rs17321999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1962588	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2089657	0.95[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2362541	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3813658	0.93[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs3817143	0.95[EUR][1000 genomes]
rs4384829	0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs4564821	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4952115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58645306	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59693338	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6708792	0.94[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6732241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72787716	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72787718	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72787719	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72787721	0.95[EUR][1000 genomes]
rs72787722	0.96[EUR][1000 genomes]
rs72787724	0.95[EUR][1000 genomes]
rs73925103	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7604484	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs906865	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs906866	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs906867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309678	0.96[EUR][1000 genomes]
rs9558	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9798481	0.94[ASN][1000 genomes]
rs9967884	0.90[CEU][hapmap]

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	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer 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	32 gene(s)	inside rSNPs	diseases
2	nsv1002657	chr2:30339312-30516535	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv2662	chr2:30462905-30495134	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30457800-30481000	Weak transcription	Gastric	stomach
2	chr2:30466200-30480400	Weak transcription	Fetal Brain Male	brain
3	chr2:30471000-30484400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:30471200-30482000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
5	chr2:30471800-30481600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:30472200-30480400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr2:30472600-30483400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr2:30473400-30480800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr2:30473400-30480800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:30474200-30480800	Enhancers	Pancreas	Pancrea
11	chr2:30474400-30481400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:30476000-30480200	Weak transcription	GM12878-XiMat	blood
13	chr2:30476200-30480200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:30476200-30481200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:30476200-30481400	Weak transcription	Esophagus	oesophagus
16	chr2:30476200-30483400	Weak transcription	Brain Anterior Caudate	brain
17	chr2:30476400-30481400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr2:30476600-30481400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:30476600-30496000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr2:30476800-30480400	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:30476800-30480400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:30476800-30480600	Weak transcription	Colonic Mucosa	Colon
23	chr2:30476800-30481400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr2:30476800-30485600	Weak transcription	Fetal Kidney	kidney
25	chr2:30477000-30481000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr2:30477000-30484200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:30477000-30488800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr2:30477200-30483800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:30477400-30481800	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr2:30477600-30480400	Weak transcription	Small Intestine	intestine
31	chr2:30477600-30483600	Strong transcription	Fetal Stomach	stomach
32	chr2:30477800-30481000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:30477800-30481000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:30477800-30482800	Strong transcription	Aorta	Aorta
35	chr2:30477800-30489000	Weak transcription	Stomach Mucosa	stomach
36	chr2:30478000-30482400	Genic enhancers	Left Ventricle	heart
37	chr2:30478000-30488400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr2:30478200-30480200	Weak transcription	Brain Germinal Matrix	brain
39	chr2:30478200-30488400	Weak transcription	Right Atrium	heart
40	chr2:30478600-30480200	Genic enhancers	Fetal Muscle Leg	muscle
41	chr2:30478600-30481400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr2:30478600-30487400	Weak transcription	K562	blood
43	chr2:30478800-30480400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr2:30478800-30484000	Strong transcription	NHLF	lung
45	chr2:30479000-30480200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr2:30479000-30480200	Weak transcription	Right Ventricle	heart
47	chr2:30479000-30481800	Strong transcription	Primary B cells from peripheral blood	blood
48	chr2:30479000-30482600	Strong transcription	Lung	lung
49	chr2:30479000-30483000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:30479000-30483400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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