Variant report

Variant	rs546872
Chromosome Location	chr1:91970335-91970336
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	chr1:91965033..91967029-chr1:91968588..91971259,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000097046	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10782970	1.00[EUR][1000 genomes]
rs11165144	1.00[EUR][1000 genomes]
rs11165243	1.00[EUR][1000 genomes]
rs12057280	1.00[EUR][1000 genomes]
rs12075049	1.00[EUR][1000 genomes]
rs13447567	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13447569	1.00[EUR][1000 genomes]
rs1508591	1.00[EUR][1000 genomes]
rs17131494	1.00[EUR][1000 genomes]
rs17131517	1.00[EUR][1000 genomes]
rs2478168	1.00[MEX][hapmap]
rs2986226	1.00[MEX][hapmap]
rs477003	0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs539048	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs544077	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6669300	1.00[EUR][1000 genomes]
rs72952927	1.00[EUR][1000 genomes]
rs7520738	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949516	chr1:91644418-92109261	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:91967200-91972000	Weak transcription	Spleen	Spleen
2	chr1:91967200-91980800	Weak transcription	Gastric	stomach
3	chr1:91967200-91989000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:91967400-91970600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:91967400-91977600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:91967400-91978200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:91967400-91984800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:91967400-91989000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:91967600-91970400	Weak transcription	Brain Substantia Nigra	brain
10	chr1:91967600-91971400	Transcr. at gene 5' and 3'	Dnd41	blood
11	chr1:91967600-91971800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:91967600-91980400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:91967600-91990600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:91967800-91976000	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:91967800-91979200	Weak transcription	Primary B cells from cord blood	blood
16	chr1:91967800-91982400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:91967800-91983000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr1:91967800-92009600	Weak transcription	Thymus	Thymus
19	chr1:91968000-91971400	Weak transcription	Placenta	Placenta
20	chr1:91968000-91973800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr1:91968000-91973800	Weak transcription	Fetal Thymus	thymus
22	chr1:91968000-91974600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:91968000-91982800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr1:91968000-91983000	Weak transcription	Fetal Muscle Leg	muscle
25	chr1:91968000-91984400	Weak transcription	Fetal Intestine Large	intestine
26	chr1:91968000-91991600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:91968200-91970600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:91968200-91973800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:91968200-91987400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr1:91968400-91973800	Weak transcription	Primary T cells from cord blood	blood
31	chr1:91968400-91979800	Weak transcription	HSMM	muscle
32	chr1:91968400-91984800	Weak transcription	NH-A	brain
33	chr1:91968400-91992000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:91968600-91970400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr1:91968600-91971000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:91968600-91971200	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr1:91968600-91974200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr1:91968600-91974200	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr1:91968600-91974200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:91968600-91974400	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr1:91968600-91974600	Weak transcription	Fetal Brain Female	brain
42	chr1:91968600-91974600	Weak transcription	HMEC	breast
43	chr1:91968600-91976200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:91968600-91977600	Weak transcription	Fetal Kidney	kidney
45	chr1:91968600-91978600	Weak transcription	NHEK	skin
46	chr1:91968600-91979200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:91968600-91979800	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:91968600-91980800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:91968600-91982600	Weak transcription	HepG2	liver
50	chr1:91968600-91984600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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