Variant report

Variant	rs550403
Chromosome Location	chr6:13409941-13409942
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13404530..13406535-chr6:13408392..13410401,3	K562	blood:
2	chr6:13408139..13410381-chr6:13486541..13489029,3	MCF-7	breast:
3	chr6:13408206..13410464-chr6:13614798..13617307,2	MCF-7	breast:
4	chr6:13408702..13411029-chr6:13413155..13415071,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261071	Chromatin interaction
ENSG00000225921	Chromatin interaction
ENSG00000145990	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10807437	0.81[ASN][1000 genomes]
rs11758233	0.81[ASN][1000 genomes]
rs1345031	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1345032	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1550520	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1550521	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2119481	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2119482	0.83[EUR][1000 genomes]
rs2119484	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2165419	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4454121	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4715251	0.90[ASN][1000 genomes]
rs4715261	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs476138	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs478630	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs478804	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs480648	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs485804	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs487607	0.81[ASN][1000 genomes]
rs488885	0.85[EUR][1000 genomes]
rs490443	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs494026	0.83[ASN][1000 genomes]
rs500197	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs500293	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs503117	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs508153	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs513613	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs519657	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs519890	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs520828	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs536916	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs536998	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs546507	0.88[ASN][1000 genomes]
rs558126	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs558242	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs559565	0.88[ASN][1000 genomes]
rs559612	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs563424	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs563662	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs564361	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs566320	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62386724	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6458814	0.88[EUR][1000 genomes]
rs6458815	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6910652	0.88[EUR][1000 genomes]
rs7742086	0.83[ASN][1000 genomes]
rs821298	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs821299	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs821300	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9370104	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9395768	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9474117	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13401800-13419000	Weak transcription	Primary B cells from peripheral blood	blood
2	chr6:13404400-13411400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:13405000-13410200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:13405000-13418400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr6:13405000-13421800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr6:13405400-13410400	Weak transcription	Aorta	Aorta
7	chr6:13408000-13410800	Enhancers	Fetal Heart	heart
8	chr6:13408600-13410200	Weak transcription	Colon Smooth Muscle	Colon
9	chr6:13408600-13411000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:13408600-13411200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:13408600-13411400	Weak transcription	Pancreas	Pancrea
12	chr6:13408600-13411800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:13408600-13412200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr6:13408600-13412400	Weak transcription	Fetal Lung	lung
15	chr6:13408600-13412400	Weak transcription	Spleen	Spleen
16	chr6:13408600-13412600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:13408600-13412800	Weak transcription	Gastric	stomach
18	chr6:13408600-13413000	Weak transcription	NHLF	lung
19	chr6:13408600-13413200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:13408600-13413200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr6:13408600-13413200	Weak transcription	Fetal Stomach	stomach
22	chr6:13408600-13413400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:13408600-13413400	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr6:13408600-13413400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr6:13408600-13413400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr6:13408600-13413600	Weak transcription	Placenta	Placenta
27	chr6:13408600-13413600	Weak transcription	Osteobl	bone
28	chr6:13408600-13414200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr6:13408600-13414600	Weak transcription	NHEK	skin
30	chr6:13408600-13415800	Enhancers	Liver	Liver
31	chr6:13408600-13422600	Weak transcription	HSMM	muscle
32	chr6:13408800-13410200	Weak transcription	Brain Hippocampus Middle	brain
33	chr6:13408800-13410200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr6:13408800-13410400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:13408800-13410400	Weak transcription	Brain Substantia Nigra	brain
36	chr6:13408800-13410400	Weak transcription	Left Ventricle	heart
37	chr6:13408800-13410400	Weak transcription	Psoas Muscle	Psoas
38	chr6:13408800-13410400	Weak transcription	Right Atrium	heart
39	chr6:13408800-13410400	Weak transcription	GM12878-XiMat	blood
40	chr6:13408800-13411200	Weak transcription	Adipose Nuclei	Adipose
41	chr6:13408800-13411200	Weak transcription	Right Ventricle	heart
42	chr6:13408800-13411400	Weak transcription	Lung	lung
43	chr6:13408800-13412400	Weak transcription	Stomach Mucosa	stomach
44	chr6:13408800-13412800	Enhancers	HepG2	liver
45	chr6:13408800-13413200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:13408800-13413200	Weak transcription	Brain Anterior Caudate	brain
47	chr6:13408800-13413400	Weak transcription	NH-A	brain
48	chr6:13408800-13413600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:13408800-13413600	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr6:13408800-13414200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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