Variant report

Variant	rs6477023
Chromosome Location	chr9:5983196-5983197
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:5982519..5984611-chr9:5989503..5991356,2	MCF-7	breast:
2	chr9:5982537..5984417-chr9:6009153..6011751,2	K562	blood:
3	chr9:5982597..5985253-chr9:6007111..6008790,2	K562	blood:

Variant related genes	Relation type
ENSG00000263575	Chromatin interaction
ENSG00000183354	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10117416	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10121480	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10733520	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10733521	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10733522	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10733523	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10739079	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10739082	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10758731	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10758732	0.83[ASN][1000 genomes]
rs10758734	0.94[EUR][1000 genomes]
rs10815330	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10815335	0.94[EUR][1000 genomes]
rs1331378	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1331379	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1478935	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1478936	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1478937	0.82[ASN][1000 genomes]
rs1478938	0.82[ASN][1000 genomes]
rs186913	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1888703	1.00[ASN][1000 genomes]
rs1888704	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2169906	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2381341	0.83[ASN][1000 genomes]
rs2381360	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2890690	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3739649	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3933800	0.82[ASN][1000 genomes]
rs4389996	0.83[ASN][1000 genomes]
rs4421399	0.81[ASN][1000 genomes]
rs4740833	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4740834	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742141	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4742142	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4742143	0.99[ASN][1000 genomes]
rs6477021	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6477022	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6477024	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6477025	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6477026	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7021498	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7024130	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7026453	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7026454	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7029054	0.80[ASN][1000 genomes]
rs7029833	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7030731	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7032130	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7044750	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851268	0.89[ASN][1000 genomes]
rs7851749	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7868062	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7869571	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7875450	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017103	chr9:5509431-5987907	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv539965	chr9:5509431-5987907	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv892155	chr9:5825768-6044937	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv892156	chr9:5892375-6011757	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1015450	chr9:5915640-6114652	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:5940000-6006800	Weak transcription	Gastric	stomach
2	chr9:5948000-6006000	Weak transcription	Right Ventricle	heart
3	chr9:5950600-6006000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:5955000-5993600	Weak transcription	Lung	lung
5	chr9:5956200-5988000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr9:5957400-6004400	Weak transcription	Brain Germinal Matrix	brain
7	chr9:5957600-5991800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr9:5958200-5986200	Weak transcription	Thymus	Thymus
9	chr9:5965400-5986800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr9:5967000-5996600	Weak transcription	Brain Angular Gyrus	brain
11	chr9:5967200-5983600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr9:5967200-6006000	Weak transcription	Colonic Mucosa	Colon
13	chr9:5968000-5987000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr9:5968200-5986200	Weak transcription	Brain Anterior Caudate	brain
15	chr9:5968400-6005600	Weak transcription	Fetal Kidney	kidney
16	chr9:5969200-5987000	Weak transcription	A549	lung
17	chr9:5969200-5996800	Weak transcription	HMEC	breast
18	chr9:5969400-5985200	Weak transcription	Placenta	Placenta
19	chr9:5969400-5985800	Weak transcription	Adipose Nuclei	Adipose
20	chr9:5969400-5987000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr9:5969400-5999600	Weak transcription	HSMMtube	muscle
22	chr9:5972200-6005800	Weak transcription	NH-A	brain
23	chr9:5972800-5986200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr9:5973600-5990600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr9:5974000-5988200	Weak transcription	Fetal Intestine Small	intestine
26	chr9:5974000-5989000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr9:5974000-5990800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr9:5974000-5991400	Weak transcription	Esophagus	oesophagus
29	chr9:5974000-6006800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr9:5974400-5999600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr9:5974800-5990600	Weak transcription	HepG2	liver
32	chr9:5974800-6001000	Weak transcription	Fetal Brain Female	brain
33	chr9:5975000-5987000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr9:5975200-5985400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr9:5975200-6005800	Weak transcription	Fetal Stomach	stomach
36	chr9:5975800-5985800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr9:5976200-5985000	Weak transcription	HSMM	muscle
38	chr9:5976200-5986000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr9:5976400-5986800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr9:5977200-5989400	Weak transcription	HUVEC	blood vessel
41	chr9:5977200-5997000	Weak transcription	Colon Smooth Muscle	Colon
42	chr9:5977400-5985000	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr9:5977400-5985400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr9:5977400-5986000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr9:5977400-5986600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr9:5977400-5987000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr9:5977400-5987400	Weak transcription	Hela-S3	cervix
48	chr9:5977400-5987800	Weak transcription	GM12878-XiMat	blood
49	chr9:5977400-5988400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr9:5977400-5993400	Weak transcription	Brain Cingulate Gyrus	brain

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