Variant report

Variant	rs2890690
Chromosome Location	chr9:5990282-5990283
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:5982519..5984611-chr9:5989503..5991356,2	MCF-7	breast:
2	chr9:5988846..5992125-chr9:6006964..6009539,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263575	Chromatin interaction
ENSG00000183354	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10117416	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10121480	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10733520	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10733521	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10733522	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10733523	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10739079	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10739082	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10758731	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10758732	0.86[ASN][1000 genomes]
rs10758734	0.94[EUR][1000 genomes]
rs10815330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10815335	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1331378	0.94[EUR][1000 genomes]
rs1331379	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1478935	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1478936	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1478937	0.81[ASN][1000 genomes]
rs1478938	0.81[ASN][1000 genomes]
rs186913	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1888703	0.95[ASN][1000 genomes]
rs1888704	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2169906	1.00[EUR][1000 genomes]
rs2381341	0.81[ASN][1000 genomes]
rs2381360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3739649	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3933800	0.80[ASN][1000 genomes]
rs4389996	0.86[ASN][1000 genomes]
rs4421399	0.82[ASN][1000 genomes]
rs4740833	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4740834	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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];0.96[ASN][1000 genomes]
rs4742143	0.96[ASN][1000 genomes]
rs6477021	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6477022	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6477023	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6477024	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6477025	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6477026	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7021498	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7024130	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7026453	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7026454	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7029833	1.00[EUR][1000 genomes];0.82[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];0.92[ASN][1000 genomes]
rs7044750	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7851268	0.93[ASN][1000 genomes]
rs7851749	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7868062	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7869571	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7875450	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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:108 , 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	chr9:5957400-6004400	Weak transcription	Brain Germinal Matrix	brain
6	chr9:5957600-5991800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr9:5967000-5996600	Weak transcription	Brain Angular Gyrus	brain
8	chr9:5967200-6006000	Weak transcription	Colonic Mucosa	Colon
9	chr9:5968400-6005600	Weak transcription	Fetal Kidney	kidney
10	chr9:5969200-5996800	Weak transcription	HMEC	breast
11	chr9:5969400-5999600	Weak transcription	HSMMtube	muscle
12	chr9:5972200-6005800	Weak transcription	NH-A	brain
13	chr9:5973600-5990600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr9:5974000-5990800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr9:5974000-5991400	Weak transcription	Esophagus	oesophagus
16	chr9:5974000-6006800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:5974400-5999600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr9:5974800-5990600	Weak transcription	HepG2	liver
19	chr9:5974800-6001000	Weak transcription	Fetal Brain Female	brain
20	chr9:5975200-6005800	Weak transcription	Fetal Stomach	stomach
21	chr9:5977200-5997000	Weak transcription	Colon Smooth Muscle	Colon
22	chr9:5977400-5993400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr9:5977400-5994400	Weak transcription	K562	blood
24	chr9:5977400-5996200	Weak transcription	Psoas Muscle	Psoas
25	chr9:5977400-5996600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr9:5977400-5996800	Weak transcription	Stomach Mucosa	stomach
27	chr9:5977400-6000800	Weak transcription	Small Intestine	intestine
28	chr9:5977400-6004800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr9:5977400-6005600	Weak transcription	NHLF	lung
30	chr9:5977400-6005800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr9:5977400-6006800	Weak transcription	Pancreas	Pancrea
32	chr9:5977400-6007000	Weak transcription	Spleen	Spleen
33	chr9:5978800-5994000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr9:5982600-5991200	Weak transcription	Aorta	Aorta
35	chr9:5982600-5995600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr9:5982800-5993600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr9:5982800-5999400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr9:5982800-6005200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr9:5983200-5993600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr9:5983200-5993600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr9:5983200-5996800	Weak transcription	NHEK	skin
42	chr9:5983200-5999400	Weak transcription	Brain Substantia Nigra	brain
43	chr9:5983200-6004200	Weak transcription	Osteobl	bone
44	chr9:5983400-5996600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr9:5983400-6004200	Weak transcription	NHDF-Ad	bronchial
46	chr9:5984000-6001000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr9:5986600-5996400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr9:5987200-5992000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr9:5987200-5993600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr9:5987200-6000800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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