Variant report

Variant	rs6561491
Chromosome Location	chr13:49551750-49551751
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:49551617..49554201-chr13:49560922..49563747,2	MCF-7	breast:
2	chr10:81106936..81108869-chr13:49549506..49551759,2	MCF-7	breast:
3	chr13:49547950..49551813-chr13:49821954..49825536,3	K562	blood:

Variant related genes	Relation type
ENSG00000201662	Chromatin interaction
ENSG00000108179	Chromatin interaction
ENSG00000102543	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs12872974	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1359066	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1407829	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1928109	0.94[EUR][1000 genomes]
rs1928110	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1937180	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2021622	0.83[EUR][1000 genomes]
rs2026029	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2146748	0.81[EUR][1000 genomes]
rs2149498	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2181537	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2181538	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2181539	0.82[EUR][1000 genomes]
rs2183095	0.94[EUR][1000 genomes]
rs2407265	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2407266	0.94[EUR][1000 genomes]
rs2897633	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2987528	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2987532	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2987535	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2994377	0.82[EUR][1000 genomes]
rs2994378	0.82[EUR][1000 genomes]
rs2994379	0.89[EUR][1000 genomes]
rs2994380	0.89[EUR][1000 genomes]
rs2994381	0.89[EUR][1000 genomes]
rs3012116	0.94[EUR][1000 genomes]
rs3012117	0.94[EUR][1000 genomes]
rs3012118	0.94[EUR][1000 genomes]
rs3012121	0.94[EUR][1000 genomes]
rs3012127	0.89[EUR][1000 genomes]
rs3012133	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3012135	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3012136	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4142065	0.83[EUR][1000 genomes]
rs4258502	0.91[ASN][1000 genomes]
rs4530025	0.81[EUR][1000 genomes]
rs4942795	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4942796	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4942798	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4942799	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4942800	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6561493	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6561496	0.82[EUR][1000 genomes]
rs7139854	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs720627	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs728075	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7318871	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7325026	0.86[EUR][1000 genomes]
rs7328000	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7329291	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7331917	0.80[EUR][1000 genomes]
rs7983885	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7986624	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7987258	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7988168	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7994368	0.87[ASN][1000 genomes]
rs7994910	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7995616	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7997118	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7998359	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7999513	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8248	0.87[ASN][1000 genomes]
rs9316426	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9316427	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9316428	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9316429	0.81[ASN][1000 genomes]
rs9526517	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9526518	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9526520	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9526521	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535126	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535133	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535136	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535140	0.85[EUR][1000 genomes]
rs9535141	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9535145	0.80[EUR][1000 genomes]
rs9535146	0.81[EUR][1000 genomes]
rs9535147	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9535149	0.82[EUR][1000 genomes]
rs9562866	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568143	0.89[ASN][1000 genomes]
rs9568150	0.82[EUR][1000 genomes]
rs9568151	0.82[EUR][1000 genomes]
rs9591235	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1034	chr13:49526761-49572727	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49548400-49552200	Active TSS	Aorta	Aorta
2	chr13:49548800-49552200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr13:49548800-49552200	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr13:49548800-49552400	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr13:49548800-49552400	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr13:49548800-49552400	Active TSS	Stomach Smooth Muscle	stomach
7	chr13:49548800-49552600	Active TSS	Fetal Intestine Large	intestine
8	chr13:49548800-49552600	Active TSS	NHDF-Ad	bronchial
9	chr13:49548800-49552800	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr13:49548800-49553000	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr13:49548800-49554800	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr13:49548800-49555800	Active TSS	Right Ventricle	heart
13	chr13:49549000-49551800	Active TSS	H9 Cell Line	embryonic stem cell
14	chr13:49549000-49552000	Active TSS	Fetal Intestine Small	intestine
15	chr13:49549000-49552000	Active TSS	Osteobl	bone
16	chr13:49549000-49552200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr13:49549000-49552400	Active TSS	NHLF	lung
18	chr13:49549000-49552600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr13:49549000-49553200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr13:49549000-49553800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr13:49549000-49554200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr13:49549200-49551800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr13:49549200-49551800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr13:49549200-49551800	Active TSS	Brain Cingulate Gyrus	brain
25	chr13:49549200-49551800	Active TSS	Brain Hippocampus Middle	brain
26	chr13:49549200-49551800	Active TSS	Fetal Heart	heart
27	chr13:49549200-49551800	Active TSS	Fetal Lung	lung
28	chr13:49549200-49552200	Active TSS	H1 Cell Line	embryonic stem cell
29	chr13:49549200-49552200	Active TSS	Colonic Mucosa	Colon
30	chr13:49549200-49552200	Active TSS	Colon Smooth Muscle	Colon
31	chr13:49549200-49552200	Active TSS	Duodenum Mucosa	Duodenum
32	chr13:49549200-49552200	Active TSS	Fetal Stomach	stomach
33	chr13:49549200-49552200	Active TSS	Left Ventricle	heart
34	chr13:49549200-49552200	Active TSS	Ovary	ovary
35	chr13:49549200-49552800	Active TSS	A549	lung
36	chr13:49549200-49553200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr13:49549200-49553400	Active TSS	Brain Anterior Caudate	brain
38	chr13:49549400-49551800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr13:49549400-49551800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
40	chr13:49549400-49551800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr13:49549400-49551800	Active TSS	Psoas Muscle	Psoas
42	chr13:49549400-49552000	Active TSS	Fetal Brain Female	brain
43	chr13:49549400-49552200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr13:49549400-49552400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr13:49549400-49552400	Active TSS	HSMM	muscle
46	chr13:49549600-49551800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr13:49549600-49551800	Active TSS	Brain Angular Gyrus	brain
48	chr13:49549600-49551800	Active TSS	Fetal Muscle Leg	muscle
49	chr13:49549600-49551800	Active TSS	Thymus	Thymus
50	chr13:49549600-49552000	Active TSS	NHEK	skin

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