Variant report

Variant	rs4454121
Chromosome Location	chr6:13404152-13404153
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1345031	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1345032	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1550520	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1550521	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2119481	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2119484	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2165419	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4715251	0.96[ASN][1000 genomes]
rs4715261	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476138	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs478630	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs478804	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs480648	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs485804	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs488885	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs490443	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs494026	0.89[ASN][1000 genomes]
rs500197	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs500293	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs503117	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs508153	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs513613	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs519657	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519890	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs520828	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs536916	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs536998	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs544639	0.83[EUR][1000 genomes]
rs546507	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs550403	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs558126	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs558242	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs559565	0.94[ASN][1000 genomes]
rs559612	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs563424	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs563662	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs564361	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566320	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62386724	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6458814	0.82[EUR][1000 genomes]
rs6458815	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6910652	0.82[EUR][1000 genomes]
rs7742086	0.89[ASN][1000 genomes]
rs821298	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs821299	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821300	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9370104	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9395768	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9474117	0.89[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:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13368000-13404600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:13396000-13404400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr6:13396200-13407000	Weak transcription	Gastric	stomach
4	chr6:13396400-13404400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:13396600-13405800	Weak transcription	HepG2	liver
6	chr6:13396800-13404400	Weak transcription	NHLF	lung
7	chr6:13397000-13404600	Weak transcription	Aorta	Aorta
8	chr6:13398000-13404400	Weak transcription	Esophagus	oesophagus
9	chr6:13398000-13404600	Weak transcription	Small Intestine	intestine
10	chr6:13398000-13406000	Weak transcription	Lung	lung
11	chr6:13398200-13406800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr6:13398400-13407400	Weak transcription	Placenta	Placenta
13	chr6:13398600-13406000	Weak transcription	Primary B cells from cord blood	blood
14	chr6:13399000-13404400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr6:13399000-13404400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:13399000-13404600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr6:13399000-13404800	Weak transcription	Spleen	Spleen
18	chr6:13399200-13404400	Weak transcription	Adipose Nuclei	Adipose
19	chr6:13399200-13404400	Weak transcription	Psoas Muscle	Psoas
20	chr6:13399200-13404400	Weak transcription	A549	lung
21	chr6:13399200-13404600	Weak transcription	HSMMtube	muscle
22	chr6:13399200-13406800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr6:13399400-13404400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:13399400-13404400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:13399400-13404400	Weak transcription	Brain Hippocampus Middle	brain
26	chr6:13399400-13404400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr6:13399400-13404400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr6:13399400-13404400	Weak transcription	NHEK	skin
29	chr6:13399400-13404600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr6:13399400-13405800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr6:13399800-13404400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr6:13400000-13404400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:13400600-13404600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr6:13401000-13406000	Weak transcription	Colon Smooth Muscle	Colon
35	chr6:13401200-13404400	Weak transcription	Right Ventricle	heart
36	chr6:13401200-13404400	Weak transcription	K562	blood
37	chr6:13401400-13404400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:13401400-13404400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:13401400-13404400	Weak transcription	HMEC	breast
40	chr6:13401600-13404400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:13401600-13404400	Weak transcription	Left Ventricle	heart
42	chr6:13401600-13404400	Weak transcription	Right Atrium	heart
43	chr6:13401600-13407000	Weak transcription	GM12878-XiMat	blood
44	chr6:13401800-13419000	Weak transcription	Primary B cells from peripheral blood	blood
45	chr6:13403200-13404600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:13403400-13404400	Weak transcription	NH-A	brain
47	chr6:13403600-13404400	Enhancers	Hela-S3	cervix
48	chr6:13403600-13404400	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr6:13403600-13404600	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr6:13403600-13409600	Enhancers	Primary monocytes fromperipheralblood	blood

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