Variant report

Variant	rs2146790
Chromosome Location	chr9:6986930-6986931
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	chr9:6986135..6988312-chr9:6992816..6995034,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10815504	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10815505	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2146791	0.83[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2146792	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2381526	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2381528	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2381529	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2381531	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2792226	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35900610	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6477135	0.87[AMR][1000 genomes]
rs7027018	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7875415	0.85[AMR][1000 genomes]
rs8181056	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs818906	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs818908	0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs818909	0.95[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs912207	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs912208	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs912209	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870402	chr9:6565246-7016784	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv1033539	chr9:6566610-7022554	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
3	nsv466111	chr9:6567841-7017391	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
4	nsv613208	chr9:6567841-7017391	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
5	nsv1024831	chr9:6573752-7018641	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
6	nsv892166	chr9:6602821-7222495	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
7	nsv892181	chr9:6680477-7070962	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
8	nsv613252	chr9:6715730-7022554	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv1023906	chr9:6731786-7372132	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv1023461	chr9:6774993-7022554	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv831500	chr9:6847952-6992535	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv831501	chr9:6868099-7058526	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv892185	chr9:6929053-7070962	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv1021234	chr9:6933222-7015397	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv870178	chr9:6941584-7060029	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv892186	chr9:6942605-7075305	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv892187	chr9:6974101-7035727	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	esv2310296	chr9:6986930-6986931	Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6890000-6987200	Weak transcription	Aorta	Aorta
2	chr9:6954200-6994800	Weak transcription	Gastric	stomach
3	chr9:6956000-6996000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr9:6960200-6987000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr9:6972000-7013200	Weak transcription	Fetal Kidney	kidney
6	chr9:6974000-6995000	Weak transcription	HMEC	breast
7	chr9:6974200-6999800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr9:6975400-6997400	Weak transcription	Fetal Heart	heart
9	chr9:6976200-7011800	Weak transcription	Psoas Muscle	Psoas
10	chr9:6977000-7008200	Strong transcription	Primary B cells from cord blood	blood
11	chr9:6977600-6999200	Strong transcription	Primary T cells from cord blood	blood
12	chr9:6977800-7008200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr9:6978800-7008200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:6979000-6993600	Weak transcription	Esophagus	oesophagus
15	chr9:6979600-6997800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr9:6979600-6998200	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr9:6979600-7008000	Weak transcription	NHEK	skin
18	chr9:6979800-7018600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr9:6980200-6998000	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr9:6980200-7008400	Strong transcription	Primary B cells from peripheral blood	blood
21	chr9:6980400-6992600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr9:6980600-6990000	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr9:6980800-6988000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr9:6980800-7004200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr9:6981000-6988800	Strong transcription	GM12878-XiMat	blood
26	chr9:6981000-6991000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr9:6981000-6997400	Strong transcription	Liver	Liver
28	chr9:6981000-6997800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr9:6981000-6998200	Strong transcription	Fetal Thymus	thymus
30	chr9:6981400-7008000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr9:6981400-7011200	Weak transcription	HUVEC	blood vessel
32	chr9:6981600-6989200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr9:6981600-6997200	Weak transcription	HSMM	muscle
34	chr9:6981600-6999000	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr9:6982000-6987000	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr9:6982400-6987600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr9:6982400-6988000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr9:6982400-6988800	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr9:6982400-6989200	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr9:6982400-6989600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr9:6982400-6996200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr9:6982600-6987600	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr9:6982600-6987600	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr9:6982600-6987600	Strong transcription	Stomach Smooth Muscle	stomach
45	chr9:6982600-6987600	Strong transcription	Thymus	Thymus
46	chr9:6982600-6988000	Strong transcription	Fetal Intestine Large	intestine
47	chr9:6982600-6989400	Strong transcription	Adipose Nuclei	Adipose
48	chr9:6982600-6997600	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr9:6982600-6998800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr9:6982600-7000200	Strong transcription	Rectal Mucosa Donor 29	rectum

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