Variant report

Variant	rs6561516
Chromosome Location	chr13:49882529-49882530
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:49882439..49884408-chr13:49887006..49888853,2	MCF-7	breast:
2	chr13:49879463..49882852-chr13:49885235..49888235,4	MCF-7	breast:
3	chr13:49882177..49886130-chr13:50015699..50019370,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136169	Chromatin interaction
ENSG00000102547	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs17072837	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17072857	1.00[EUR][1000 genomes]
rs17072868	1.00[EUR][1000 genomes]
rs1983806	0.89[CHD][hapmap];0.89[JPT][hapmap]
rs2181906	0.82[ASN][1000 genomes]
rs3990408	0.96[ASN][1000 genomes]
rs60882749	0.96[ASN][1000 genomes]
rs6561498	0.89[CHD][hapmap];0.89[JPT][hapmap]
rs7321706	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs74074564	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7999767	0.89[JPT][hapmap]
rs912193	0.82[ASN][1000 genomes]
rs912547	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535196	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv832607	chr13:49756458-49920894	Flanking Bivalent TSS/Enh Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv900069	chr13:49815405-49976393	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49854000-49883000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr13:49867200-49884200	Weak transcription	Fetal Brain Female	brain
3	chr13:49875800-49883800	Weak transcription	Fetal Intestine Small	intestine
4	chr13:49875800-49884000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr13:49875800-49884200	Weak transcription	Primary T cells from cord blood	blood
6	chr13:49875800-49887800	Weak transcription	Fetal Intestine Large	intestine
7	chr13:49875800-49887800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr13:49875800-49891000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr13:49876000-49884000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr13:49876200-49884200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr13:49876200-49884200	Weak transcription	Brain Germinal Matrix	brain
12	chr13:49876200-49895000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr13:49876200-49935600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr13:49876400-49887800	Weak transcription	Colonic Mucosa	Colon
15	chr13:49876400-49887800	Weak transcription	Fetal Heart	heart
16	chr13:49876400-49887800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr13:49877200-49883800	Enhancers	Adipose Nuclei	Adipose
18	chr13:49878000-49882600	Weak transcription	Fetal Thymus	thymus
19	chr13:49878200-49893600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr13:49878200-49894800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr13:49878400-49882600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr13:49878400-49882600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr13:49878400-49888000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr13:49878800-49884200	Weak transcription	Gastric	stomach
25	chr13:49879000-49887800	Weak transcription	Spleen	Spleen
26	chr13:49879200-49883600	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr13:49879400-49883600	Enhancers	Fetal Muscle Leg	muscle
28	chr13:49879800-49883600	Enhancers	Fetal Muscle Trunk	muscle
29	chr13:49880200-49882800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr13:49880200-49885800	Weak transcription	Fetal Kidney	kidney
31	chr13:49880400-49883600	Enhancers	Ovary	ovary
32	chr13:49880400-49894200	Weak transcription	Primary B cells from cord blood	blood
33	chr13:49880600-49888600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr13:49880600-49896000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr13:49881000-49884000	Enhancers	Stomach Smooth Muscle	stomach
36	chr13:49881400-49882800	Enhancers	Stomach Mucosa	stomach
37	chr13:49881400-49883000	Enhancers	Fetal Stomach	stomach
38	chr13:49881400-49883400	Enhancers	Fetal Lung	lung
39	chr13:49881400-49883600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr13:49881400-49884600	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr13:49881600-49882600	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr13:49881600-49882800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr13:49881600-49882800	Enhancers	Aorta	Aorta
44	chr13:49881600-49882800	Enhancers	Lung	lung
45	chr13:49881600-49882800	Enhancers	Right Atrium	heart
46	chr13:49881600-49883000	Enhancers	Psoas Muscle	Psoas
47	chr13:49881600-49883000	Enhancers	Right Ventricle	heart
48	chr13:49881600-49883400	Enhancers	NHLF	lung
49	chr13:49881600-49883600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr13:49881600-49883600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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