Variant report

Variant	rs2040093
Chromosome Location	chr9:95950323-95950324
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95943032..95944544-chr9:95948872..95951081,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10761203	0.88[CEU][hapmap]
rs10821080	0.92[CEU][hapmap];0.91[CHB][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10821083	0.95[YRI][hapmap];0.96[AFR][1000 genomes]
rs10821084	0.86[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs10821086	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821088	0.89[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10821090	0.81[JPT][hapmap]
rs10821095	0.89[CEU][hapmap]
rs10821098	0.92[CEU][hapmap]
rs10992662	0.80[EUR][1000 genomes]
rs10992669	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992674	0.81[JPT][hapmap]
rs10992698	0.87[CEU][hapmap]
rs1106024	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1109495	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1109496	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336667	0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12341303	0.92[CEU][hapmap]
rs12349094	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1317698	0.89[CEU][hapmap]
rs13292831	0.86[CEU][hapmap]
rs13293217	0.92[CEU][hapmap]
rs1962428	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2040094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2211535	0.81[JPT][hapmap]
rs2306183	0.89[CEU][hapmap]
rs4524855	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743911	0.81[CEU][hapmap]
rs4744185	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744186	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4744188	0.82[CHB][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes]
rs4744195	0.92[CEU][hapmap]
rs4744201	0.92[CEU][hapmap]
rs4744206	0.86[CEU][hapmap]
rs4744212	0.86[CEU][hapmap]
rs56039014	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62571716	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7846729	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7856802	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7857039	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7857937	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7868971	0.89[CEU][hapmap]

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	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer 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 target site	30 gene(s)	inside rSNPs	diseases
2	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv824983	chr9:95902154-95978408	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv614880	chr9:95930572-95978265	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95947400-95950400	Enhancers	Gastric	stomach
2	chr9:95947600-95950400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr9:95947800-95950400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr9:95947800-95950400	Flanking Active TSS	Fetal Brain Female	brain
5	chr9:95947800-95950600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr9:95947800-95951800	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr9:95948200-95958400	Weak transcription	Lung	lung
8	chr9:95948400-95955200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr9:95948600-95950400	Enhancers	Fetal Intestine Large	intestine
10	chr9:95948600-95950600	Genic enhancers	Fetal Intestine Small	intestine
11	chr9:95948600-95951200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr9:95948800-95951000	Bivalent Enhancer	Fetal Stomach	stomach
13	chr9:95948800-95953000	Enhancers	Right Ventricle	heart
14	chr9:95948800-95955000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr9:95948800-95955800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr9:95949200-95950800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr9:95949200-95955800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr9:95949400-95950400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:95949600-95951000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr9:95949600-95951600	Enhancers	Brain Hippocampus Middle	brain
21	chr9:95949600-95955600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr9:95949800-95950400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr9:95949800-95950400	Enhancers	Spleen	Spleen
24	chr9:95949800-95950400	Enhancers	HepG2	liver
25	chr9:95949800-95950800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:95949800-95951200	Enhancers	Fetal Brain Male	brain
27	chr9:95949800-95951600	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr9:95949800-95952000	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr9:95949800-95954600	Weak transcription	Right Atrium	heart
30	chr9:95950000-95950400	Enhancers	Fetal Heart	heart
31	chr9:95950000-95950400	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr9:95950000-95950600	Enhancers	Brain Angular Gyrus	brain
33	chr9:95950000-95951000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr9:95950000-95951000	Weak transcription	Psoas Muscle	Psoas
35	chr9:95950000-95951200	Enhancers	Colonic Mucosa	Colon
36	chr9:95950000-95951200	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr9:95950000-95951600	Enhancers	Brain Anterior Caudate	brain
38	chr9:95950000-95952000	Enhancers	Rectal Smooth Muscle	rectum
39	chr9:95950000-95953000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr9:95950000-95953800	Enhancers	Left Ventricle	heart
41	chr9:95950000-95954000	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr9:95950000-95960800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:95950200-95950400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr9:95950200-95950400	Enhancers	Brain Germinal Matrix	brain
45	chr9:95950200-95950800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr9:95950200-95950800	Enhancers	Duodenum Mucosa	Duodenum
47	chr9:95950200-95951600	Enhancers	Colon Smooth Muscle	Colon
48	chr9:95950200-95951600	Enhancers	Stomach Mucosa	stomach
49	chr9:95950200-95954000	Enhancers	Pancreas	Pancrea

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