Variant report

Variant	rs6424640
Chromosome Location	chr1:78466644-78466645
allele	A/T
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:7)
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	RPC155	chr1:78466208-78466879	Hela-S3	cervix:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:78466521..78469448-chr1:78786020..78788848,2	K562	blood:
2	chr1:78466456..78468049-chr1:78560213..78561822,2	K562	blood:
3	chr1:78466099..78472038-chr1:78511575..78517585,8	K562	blood:
4	chr1:78441900..78447727-chr1:78466477..78473207,15	MCF-7	breast:
5	chr1:78466262..78468828-chr1:85227463..85229470,2	K562	blood:
6	chr1:78287859..78289541-chr1:78464426..78466879,2	K562	blood:
7	chr1:78245914..78248830-chr1:78466317..78468664,2	K562	blood:

No data

Variant related genes	Relation type
DNAJB4	TF binding region
ENSG00000162616	Chromatin interaction
ENSG00000137960	Chromatin interaction
ENSG00000202263	Chromatin interaction
ENSG00000162613	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1001070	0.83[AMR][1000 genomes]
rs1001103	0.85[AMR][1000 genomes]
rs1001104	0.85[AMR][1000 genomes]
rs10437022	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10873960	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873963	0.87[AMR][1000 genomes]
rs11162400	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11162403	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162406	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1166697	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1166701	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1166702	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1166704	0.84[AMR][1000 genomes]
rs1166705	0.87[AMR][1000 genomes]
rs1166706	0.87[AMR][1000 genomes]
rs1166707	0.90[AMR][1000 genomes]
rs11805735	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11807240	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12146104	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12405212	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12409561	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12723748	0.84[AMR][1000 genomes]
rs1335481	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1536160	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1555798	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1616949	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17383213	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17387365	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1855704	0.85[AMR][1000 genomes]
rs1971368	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2136682	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2274257	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2296453	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3767028	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4370803	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4372306	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4631748	0.87[AMR][1000 genomes]
rs4949828	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4949829	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57421725	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6424650	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6424660	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6424664	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6424668	0.82[AMR][1000 genomes]
rs6656888	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6677890	0.85[AMR][1000 genomes]
rs6686230	0.82[AMR][1000 genomes]
rs750720	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7514007	0.87[AMR][1000 genomes]
rs7538210	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9324166	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9659938	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9661193	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9730688	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[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	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

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78446200-78469600	Weak transcription	Thymus	Thymus
2	chr1:78446400-78469800	Weak transcription	Primary B cells from peripheral blood	blood
3	chr1:78446400-78470200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:78446600-78468000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:78446600-78468400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:78446600-78468800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:78446600-78468800	Weak transcription	Adipose Nuclei	Adipose
8	chr1:78446600-78468800	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr1:78446600-78469000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:78446600-78469000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:78446600-78469000	Weak transcription	Fetal Kidney	kidney
12	chr1:78446600-78469600	Weak transcription	Aorta	Aorta
13	chr1:78446600-78469800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:78446600-78470200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr1:78446600-78470400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:78446800-78468000	Weak transcription	Fetal Lung	lung
17	chr1:78447000-78467800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:78447600-78469800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:78447600-78470200	Weak transcription	Fetal Brain Male	brain
20	chr1:78447800-78469600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:78448000-78467800	Weak transcription	Dnd41	blood
22	chr1:78448000-78467800	Weak transcription	HUVEC	blood vessel
23	chr1:78448000-78468800	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:78448800-78488200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:78450200-78469600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:78450200-78469600	Weak transcription	Fetal Intestine Large	intestine
27	chr1:78451000-78468400	Weak transcription	Brain Anterior Caudate	brain
28	chr1:78451800-78468400	Weak transcription	HSMMtube	muscle
29	chr1:78452400-78468800	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr1:78452400-78468800	Weak transcription	Colon Smooth Muscle	Colon
31	chr1:78452800-78468400	Weak transcription	K562	blood
32	chr1:78452800-78468800	Weak transcription	NH-A	brain
33	chr1:78452800-78470400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:78452800-78478800	Weak transcription	Spleen	Spleen
35	chr1:78453000-78469600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:78454200-78468400	Weak transcription	Right Atrium	heart
37	chr1:78454200-78468800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr1:78454200-78469200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:78454200-78469800	Weak transcription	Left Ventricle	heart
40	chr1:78454200-78469800	Weak transcription	Psoas Muscle	Psoas
41	chr1:78454200-78485600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:78454400-78469800	Weak transcription	Right Ventricle	heart
43	chr1:78455600-78469200	Weak transcription	Primary B cells from cord blood	blood
44	chr1:78455800-78468800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:78456000-78468600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr1:78456000-78469200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr1:78456200-78470400	Weak transcription	Esophagus	oesophagus
48	chr1:78456600-78468800	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr1:78457400-78469000	Weak transcription	GM12878-XiMat	blood
50	chr1:78457400-78469800	Weak transcription	Ovary	ovary

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