Variant report

Variant	rs9679089
Chromosome Location	chr2:233585327-233585328
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:233560643..233562547-chr2:233584508..233586185,2	MCF-7	breast:
2	chr2:233582922..233585762-chr2:233588795..233591759,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204120	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1022330	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1044480	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10933409	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11555646	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11679079	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11687128	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11690474	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11692545	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12472839	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12474040	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12478564	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12987513	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12990821	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12991088	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12997185	0.85[EUR][1000 genomes]
rs13003675	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13004406	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13007783	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13008942	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13011298	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13013142	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13021246	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13024793	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13035829	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13424351	0.90[EUR][1000 genomes]
rs1446308	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1801251	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1867778	0.83[EUR][1000 genomes]
rs2012221	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2592105	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2592113	0.86[EUR][1000 genomes]
rs2674839	0.86[EUR][1000 genomes]
rs283468	0.84[EUR][1000 genomes]
rs283469	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs283471	0.84[EUR][1000 genomes]
rs283474	0.84[EUR][1000 genomes]
rs283475	0.84[EUR][1000 genomes]
rs283476	0.84[EUR][1000 genomes]
rs283477	0.83[EUR][1000 genomes]
rs283479	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs283480	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs283481	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs283484	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs283485	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs283486	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs33980184	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34880628	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35085837	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35212961	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35285732	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35362030	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35395584	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35621474	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36007169	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3817311	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4452130	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4458205	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4517962	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4973053	0.86[EUR][1000 genomes]
rs56777991	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66549961	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67013068	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6714245	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6717841	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6724117	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6732136	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6733151	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6738386	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6739638	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6745879	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6746294	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6747645	0.91[EUR][1000 genomes]
rs6748027	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6761324	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71421663	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs737028	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7558609	0.81[EUR][1000 genomes]
rs7562712	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7578299	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7591176	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7592717	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7606090	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs778166	0.89[EUR][1000 genomes]
rs9653383	0.86[EUR][1000 genomes]
rs983430	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]

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	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233564000-233589000	Weak transcription	NH-A	brain
2	chr2:233564200-233596400	Weak transcription	NHLF	lung
3	chr2:233564200-233613000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:233564800-233592800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:233565000-233612200	Weak transcription	Fetal Brain Male	brain
6	chr2:233565200-233589800	Weak transcription	HMEC	breast
7	chr2:233565200-233602000	Weak transcription	HUVEC	blood vessel
8	chr2:233565200-233606400	Weak transcription	Stomach Mucosa	stomach
9	chr2:233565400-233589800	Weak transcription	Hela-S3	cervix
10	chr2:233565400-233590000	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:233565600-233641000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:233566800-233612800	Weak transcription	Small Intestine	intestine
13	chr2:233568000-233604400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr2:233568200-233585400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr2:233569000-233585600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr2:233569200-233589000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:233569200-233590000	Weak transcription	NHDF-Ad	bronchial
18	chr2:233569200-233615000	Weak transcription	Colonic Mucosa	Colon
19	chr2:233569400-233612800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr2:233569400-233615400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:233570600-233593400	Weak transcription	Aorta	Aorta
22	chr2:233571200-233593600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:233571200-233598200	Weak transcription	Fetal Kidney	kidney
24	chr2:233571200-233627400	Weak transcription	Gastric	stomach
25	chr2:233571400-233585600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr2:233571400-233588600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:233571400-233601800	Weak transcription	Esophagus	oesophagus
28	chr2:233571600-233585600	Weak transcription	Right Ventricle	heart
29	chr2:233571600-233612200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr2:233572200-233585600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:233572200-233589000	Weak transcription	Osteobl	bone
32	chr2:233572200-233589800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr2:233572200-233589800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr2:233572200-233591600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr2:233572200-233593200	Weak transcription	Brain Hippocampus Middle	brain
36	chr2:233572400-233585600	Weak transcription	K562	blood
37	chr2:233572400-233585800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr2:233572400-233586800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:233573600-233589800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr2:233573800-233588600	Weak transcription	Lung	lung
41	chr2:233574000-233585600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr2:233574200-233585800	Weak transcription	NHEK	skin
43	chr2:233574200-233588800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr2:233574200-233589000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:233574200-233589200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr2:233574400-233588200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:233574400-233593400	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr2:233575400-233586800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr2:233576000-233589000	Weak transcription	Brain Germinal Matrix	brain
50	chr2:233577000-233585800	Strong transcription	Fetal Thymus	thymus

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