Variant report

Variant	rs1228040
Chromosome Location	chr11:48046692-48046693
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	chr11:48046572..48047306-chr11:48130972..48131586,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1228026	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1228028	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1228031	0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1228032	0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1228036	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1228038	0.87[YRI][hapmap];1.00[EUR][1000 genomes]
rs1228039	0.87[YRI][hapmap];1.00[EUR][1000 genomes]
rs1228042	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1234904	0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1237924	1.00[EUR][1000 genomes]
rs1238706	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs1630025	1.00[EUR][1000 genomes]
rs1681623	0.88[YRI][hapmap];1.00[EUR][1000 genomes]
rs1681624	1.00[EUR][1000 genomes]
rs1681625	0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs1729286	0.88[YRI][hapmap];1.00[EUR][1000 genomes]
rs1729288	0.91[YRI][hapmap]
rs1729291	0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs2626565	0.88[YRI][hapmap];1.00[EUR][1000 genomes]
rs2930193	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2930194	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2930197	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2950891	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73462886	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1036451	chr11:47902321-48616646	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv541037	chr11:47902321-48616646	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1047490	chr11:47916708-48388686	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1044266	chr11:47929586-48276132	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv541038	chr11:47929586-48276132	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv1053145	chr11:47967902-48086950	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv870381	chr11:47989434-48142648	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
11	esv3396029	chr11:47993857-48241494	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS 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	6 gene(s)	inside rSNPs	diseases
12	nsv897327	chr11:48004369-48911660	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
13	nsv869124	chr11:48014539-48783113	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
14	nsv1051805	chr11:48016488-48378048	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
15	nsv428573	chr11:48032457-48152344	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
16	nsv897328	chr11:48043053-48901553	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:48035600-48053000	Weak transcription	Thymus	Thymus
2	chr11:48035600-48056600	Weak transcription	HSMM	muscle
3	chr11:48038000-48052400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr11:48040000-48050600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr11:48040000-48050800	Weak transcription	Osteobl	bone
6	chr11:48040600-48047200	Weak transcription	Right Ventricle	heart
7	chr11:48040600-48053200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr11:48040800-48050400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr11:48040800-48050400	Weak transcription	NH-A	brain
10	chr11:48040800-48050600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr11:48040800-48053000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr11:48041200-48047000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:48041200-48047400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr11:48041200-48050400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr11:48041200-48050400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr11:48041400-48047200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr11:48041400-48050400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr11:48041400-48050600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr11:48041400-48051400	Weak transcription	Fetal Lung	lung
20	chr11:48041600-48047600	Weak transcription	Primary T cells from cord blood	blood
21	chr11:48042000-48050800	Weak transcription	Fetal Kidney	kidney
22	chr11:48042200-48050400	Weak transcription	Liver	Liver
23	chr11:48042200-48050400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr11:48042200-48051200	Weak transcription	Fetal Intestine Large	intestine
25	chr11:48042400-48047000	Weak transcription	Lung	lung
26	chr11:48042400-48047200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr11:48042400-48049400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr11:48042400-48049400	Weak transcription	Colonic Mucosa	Colon
29	chr11:48042400-48050400	Weak transcription	Adipose Nuclei	Adipose
30	chr11:48042400-48050400	Weak transcription	Placenta	Placenta
31	chr11:48042400-48050400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr11:48042400-48050600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr11:48042600-48047200	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr11:48042600-48049600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr11:48042600-48049600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr11:48042600-48049600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr11:48042600-48049800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr11:48043400-48049800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr11:48043600-48052800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr11:48044600-48047000	Weak transcription	Spleen	Spleen
41	chr11:48044600-48050200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr11:48044600-48050400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr11:48044800-48046800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr11:48044800-48049800	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr11:48045000-48049600	Weak transcription	GM12878-XiMat	blood
46	chr11:48045000-48053000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr11:48045200-48047800	Enhancers	Fetal Brain Female	brain
48	chr11:48045600-48047000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr11:48045600-48047400	Enhancers	Fetal Brain Male	brain
50	chr11:48045600-48047400	Enhancers	Psoas Muscle	Psoas

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