Variant report

Variant	rs561276
Chromosome Location	chr6:33543116-33543117
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	chr6:33541749..33544429-chr6:33546198..33547784,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs12529825	1.00[JPT][hapmap]
rs1536042	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16869178	1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1705000	1.00[ASN][1000 genomes]
rs1755041	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1755042	1.00[ASN][1000 genomes]
rs1755054	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17627049	0.84[YRI][hapmap]
rs1794686	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1794688	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2068236	1.00[ASN][1000 genomes]
rs2147655	1.00[ASN][1000 genomes]
rs2395451	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4711333	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4711334	1.00[ASN][1000 genomes]
rs4713647	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4713652	1.00[ASN][1000 genomes]
rs472990	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs480568	1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485623	1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs535584	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs542056	1.00[ASN][1000 genomes]
rs542725	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs549719	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55700437	1.00[ASN][1000 genomes]
rs557559	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs560218	1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs572824	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59572422	1.00[ASN][1000 genomes]
rs61687548	1.00[ASN][1000 genomes]
rs6900438	1.00[ASN][1000 genomes]
rs6906810	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928341	1.00[ASN][1000 genomes]
rs71536195	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7752930	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7757391	1.00[ASN][1000 genomes]
rs7757722	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7759154	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762843	1.00[JPT][hapmap]
rs7775313	1.00[ASN][1000 genomes]
rs806604	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs806605	0.89[EUR][1000 genomes]
rs9368770	1.00[ASN][1000 genomes]
rs9689326	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv462896	chr6:33534880-33588147	Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv602833	chr6:33534880-33588147	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33539200-33547200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:33539600-33546200	Weak transcription	NHDF-Ad	bronchial
3	chr6:33539600-33546400	Weak transcription	Fetal Brain Male	brain
4	chr6:33539600-33547000	Weak transcription	Fetal Kidney	kidney
5	chr6:33539800-33544400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:33539800-33544400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr6:33539800-33545400	Strong transcription	Fetal Intestine Small	intestine
8	chr6:33539800-33546400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:33539800-33547000	Weak transcription	Psoas Muscle	Psoas
10	chr6:33540000-33543800	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr6:33540000-33544200	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:33540000-33545000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:33540000-33545000	Weak transcription	Right Atrium	heart
14	chr6:33540000-33546400	Strong transcription	Fetal Stomach	stomach
15	chr6:33540200-33543200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:33540200-33543600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:33540200-33544800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:33540200-33545000	Strong transcription	Lung	lung
19	chr6:33540200-33545800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:33540200-33545800	Strong transcription	Fetal Muscle Leg	muscle
21	chr6:33540200-33546000	Weak transcription	Fetal Heart	heart
22	chr6:33540400-33544400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:33540400-33544400	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr6:33540400-33544600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:33540400-33544600	Strong transcription	Fetal Thymus	thymus
26	chr6:33540400-33544800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:33540600-33543800	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr6:33540800-33544600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr6:33540800-33544600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr6:33540800-33544600	Strong transcription	Adipose Nuclei	Adipose
31	chr6:33541000-33543800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr6:33541000-33544600	Strong transcription	Colonic Mucosa	Colon
33	chr6:33541000-33544800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:33541000-33545200	Strong transcription	Fetal Muscle Trunk	muscle
35	chr6:33541000-33545400	Strong transcription	Brain Germinal Matrix	brain
36	chr6:33541200-33544000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr6:33541200-33544400	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr6:33541200-33544400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr6:33541200-33544600	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr6:33541200-33544600	Strong transcription	Spleen	Spleen
41	chr6:33541200-33544800	Strong transcription	Primary B cells from peripheral blood	blood
42	chr6:33541200-33545000	Strong transcription	Stomach Smooth Muscle	stomach
43	chr6:33541200-33545000	Strong transcription	Dnd41	blood
44	chr6:33541200-33545800	Strong transcription	Fetal Brain Female	brain
45	chr6:33541200-33546000	Strong transcription	Osteobl	bone
46	chr6:33541200-33546400	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr6:33541400-33543800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:33541400-33544000	Strong transcription	Brain Substantia Nigra	brain
49	chr6:33541400-33544000	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr6:33541400-33544400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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