Variant report

Variant	rs6561495
Chromosome Location	chr13:49661997-49661998
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:49660417..49663395-chr13:49676657..49679527,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1407826	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1937182	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1983806	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2181906	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2987534	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3012124	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3012130	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3012134	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942806	0.90[ASN][1000 genomes]
rs4942807	1.00[AMR][1000 genomes]
rs57277286	1.00[AMR][1000 genomes]
rs57590763	1.00[AMR][1000 genomes]
rs58064396	1.00[AMR][1000 genomes]
rs58372993	1.00[AMR][1000 genomes]
rs61192069	1.00[AMR][1000 genomes]
rs61517389	1.00[AMR][1000 genomes]
rs6561498	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561508	1.00[AMR][1000 genomes]
rs6650333	1.00[AMR][1000 genomes]
rs7321706	1.00[EUR][1000 genomes]
rs7326409	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7338704	1.00[CHB][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7999767	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs912193	0.85[ASN][1000 genomes]
rs928039	1.00[ASN][1000 genomes]
rs9316432	1.00[AMR][1000 genomes]

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	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	nsv455882	chr13:49531551-49679157	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv561593	chr13:49531551-49679157	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv1793883	chr13:49543723-49789164	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv976274	chr13:49655803-49666815	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1035	chr13:49656225-49700371	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49627400-49672400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr13:49629000-49665600	Weak transcription	Lung	lung
3	chr13:49629600-49665400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr13:49630400-49664000	Weak transcription	Fetal Intestine Small	intestine
5	chr13:49632200-49664800	Weak transcription	Fetal Lung	lung
6	chr13:49635000-49664400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr13:49636800-49667800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr13:49639600-49687200	Weak transcription	Pancreas	Pancrea
9	chr13:49640600-49683800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr13:49641200-49663200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr13:49641800-49671600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr13:49645000-49671000	Weak transcription	Small Intestine	intestine
13	chr13:49649400-49684200	Weak transcription	Right Ventricle	heart
14	chr13:49649800-49671600	Weak transcription	Brain Hippocampus Middle	brain
15	chr13:49651400-49665600	Weak transcription	Fetal Thymus	thymus
16	chr13:49651400-49666800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr13:49651600-49663800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr13:49651600-49670200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr13:49651600-49670800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr13:49651800-49664800	Weak transcription	Fetal Stomach	stomach
21	chr13:49651800-49665000	Weak transcription	Fetal Muscle Leg	muscle
22	chr13:49651800-49671000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr13:49651800-49671800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr13:49651800-49684000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr13:49651800-49684000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr13:49652000-49667600	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr13:49652000-49671000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr13:49652400-49671600	Weak transcription	Spleen	Spleen
29	chr13:49655200-49667400	Weak transcription	HepG2	liver
30	chr13:49655600-49684200	Weak transcription	Primary B cells from peripheral blood	blood
31	chr13:49656000-49673000	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr13:49657200-49671600	Weak transcription	Ovary	ovary
33	chr13:49657200-49672200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr13:49657200-49692400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr13:49657400-49662400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr13:49657400-49665600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr13:49657400-49668200	Weak transcription	Thymus	Thymus
38	chr13:49657400-49670800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr13:49657400-49670800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr13:49657400-49670800	Weak transcription	Aorta	Aorta
41	chr13:49657400-49671200	Weak transcription	HSMM	muscle
42	chr13:49657400-49671600	Weak transcription	Left Ventricle	heart
43	chr13:49657400-49674800	Weak transcription	Fetal Intestine Large	intestine
44	chr13:49657400-49674800	Weak transcription	Placenta	Placenta
45	chr13:49657400-49684000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr13:49657600-49662000	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr13:49657600-49670200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr13:49657600-49670800	Weak transcription	Liver	Liver
49	chr13:49657800-49683800	Weak transcription	Primary B cells from cord blood	blood
50	chr13:49658000-49665600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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