Variant report

Variant	rs6424648
Chromosome Location	chr1:78475199-78475200
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	CEBPB	chr1:78475002-78475394	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:78475016-78475424	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:78468129..78475881-chr1:78555411..78565499,18	K562	blood:
2	chr1:78474613..78477599-chr1:78511553..78513416,2	K562	blood:
3	chr1:78474587..78476658-chr1:78580755..78582747,2	K562	blood:
4	chr1:78472904..78475417-chr1:78568787..78572240,3	K562	blood:

Variant related genes	Relation type
ENSG00000273338	TF binding region
ENSG00000202263	Chromatin interaction
ENSG00000213560	Chromatin interaction
ENSG00000137960	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1039863	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[ASN][1000 genomes]
rs10735751	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10873961	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10873962	0.83[ASN][1000 genomes]
rs10873963	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.82[YRI][hapmap];0.83[ASN][1000 genomes]
rs11162401	0.91[ASN][1000 genomes]
rs1166696	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1166699	0.89[ASN][1000 genomes]
rs1166700	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11805942	0.91[ASN][1000 genomes]
rs11806130	0.93[ASN][1000 genomes]
rs11811805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1510244	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17101101	0.91[ASN][1000 genomes]
rs1749911	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1749913	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1780044	1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1780045	1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1780047	1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1780048	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1780052	0.81[AMR][1000 genomes]
rs2296452	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2296454	1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3736909	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3767024	1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3767025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3790586	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4083559	0.88[ASN][1000 genomes]
rs4107671	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4483454	0.89[ASN][1000 genomes]
rs4543852	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4631748	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]
rs4949823	0.82[CHB][hapmap]
rs6424653	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6604878	0.82[CHB][hapmap]
rs6675105	1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap]
rs6680447	0.92[ASN][1000 genomes]
rs6699513	0.83[ASN][1000 genomes]
rs6702465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685363	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72685364	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72685368	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7520255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7523874	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7524504	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7547599	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs9661687	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9662129	0.93[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9729146	0.93[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][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	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	esv1801396	chr1:78468094-78492221	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78448800-78488200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:78452800-78478800	Weak transcription	Spleen	Spleen
3	chr1:78454200-78485600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:78468400-78475800	Active TSS	Right Atrium	heart
5	chr1:78469200-78475400	Active TSS	NHLF	lung
6	chr1:78469400-78475400	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr1:78469600-78476400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:78469600-78476800	Active TSS	HSMMtube	muscle
9	chr1:78469600-78477200	Active TSS	Aorta	Aorta
10	chr1:78469800-78476800	Active TSS	Stomach Smooth Muscle	stomach
11	chr1:78469800-78477400	Active TSS	Right Ventricle	heart
12	chr1:78470800-78487800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:78471000-78487400	Weak transcription	Lung	lung
14	chr1:78471200-78486400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:78471600-78483000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:78471600-78483400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:78471600-78483800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:78471600-78487000	Weak transcription	Primary B cells from peripheral blood	blood
19	chr1:78471800-78477200	Transcr. at gene 5' and 3'	HSMM	muscle
20	chr1:78471800-78482000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:78472000-78478800	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr1:78472000-78479200	Weak transcription	Fetal Brain Male	brain
23	chr1:78472000-78484800	Weak transcription	Colonic Mucosa	Colon
24	chr1:78472000-78487000	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr1:78472200-78484200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:78472400-78483200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:78472400-78486800	Weak transcription	Fetal Thymus	thymus
28	chr1:78472600-78476800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr1:78472600-78478600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:78472600-78478800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:78472600-78479800	Weak transcription	Fetal Stomach	stomach
32	chr1:78472800-78475800	Enhancers	Liver	Liver
33	chr1:78472800-78477000	Enhancers	HepG2	liver
34	chr1:78472800-78478600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:78472800-78478600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:78472800-78478800	Weak transcription	Placenta	Placenta
37	chr1:78472800-78481600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:78472800-78482000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:78472800-78486400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr1:78473000-78475600	Weak transcription	Fetal Intestine Large	intestine
41	chr1:78473800-78476400	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr1:78473800-78477000	Active TSS	GM12878-XiMat	blood
43	chr1:78473800-78480200	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr1:78473800-78487000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:78474000-78475200	Enhancers	Fetal Heart	heart
46	chr1:78474000-78475200	Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr1:78474000-78475400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr1:78474000-78475600	Weak transcription	Rectal Smooth Muscle	rectum
49	chr1:78474000-78475800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr1:78474000-78478600	Weak transcription	Fetal Muscle Trunk	muscle

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