Variant report

Variant	rs513613
Chromosome Location	chr6:13398144-13398145
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:13396129..13398707-chr6:13570124..13572077,2	MCF-7	breast:
2	chr6:13396704..13399515-chr6:13413657..13416189,2	K562	blood:
3	chr6:13397579..13400126-chr6:13573111..13574727,2	MCF-7	breast:
4	chr6:13354231..13355859-chr6:13396144..13399097,2	K562	blood:
5	chr6:13397740..13400586-chr6:13613823..13615794,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PHACTR1-3	chr6:13398040-13398381	expReg_chr6_942_+

No data

Variant related genes	Relation type
ENSG00000261071	Chromatin interaction
ENSG00000225921	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11753720	0.89[ASN][1000 genomes]
rs1345031	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1345032	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1837701	0.89[ASN][1000 genomes]
rs2119483	0.89[ASN][1000 genomes]
rs2119484	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4454121	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4715251	0.85[ASN][1000 genomes]
rs4715261	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs476138	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs478630	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs478804	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs480648	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs485804	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs488885	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs490443	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs500197	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500293	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs503117	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs508153	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs519657	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs519890	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs520828	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs523221	0.89[ASN][1000 genomes]
rs536916	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs536998	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs544639	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs546507	0.83[ASN][1000 genomes]
rs550403	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs558126	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs558242	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs559565	0.83[ASN][1000 genomes]
rs559612	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs563424	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs563662	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564361	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs565013	0.89[ASN][1000 genomes]
rs566320	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62386724	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62386725	0.89[ASN][1000 genomes]
rs62386727	0.87[ASN][1000 genomes]
rs821298	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821299	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs821300	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357720	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:66 , 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	chr6:13394600-13399000	Enhancers	Primary B cells from peripheral blood	blood
3	chr6:13395000-13399000	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr6:13395200-13398600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr6:13395200-13398800	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr6:13395200-13398800	Enhancers	Stomach Mucosa	stomach
7	chr6:13395200-13399000	Enhancers	Primary hematopoietic stem cells	blood
8	chr6:13395200-13399200	Enhancers	Adipose Nuclei	Adipose
9	chr6:13395400-13398200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:13395400-13398200	Enhancers	Duodenum Mucosa	Duodenum
11	chr6:13395400-13398400	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr6:13395400-13398400	Enhancers	Right Atrium	heart
13	chr6:13395400-13398600	Enhancers	Primary B cells from cord blood	blood
14	chr6:13395400-13398600	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr6:13395400-13399000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:13395400-13399000	Enhancers	Spleen	Spleen
17	chr6:13395400-13399200	Enhancers	Psoas Muscle	Psoas
18	chr6:13395400-13399200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr6:13395400-13399200	Enhancers	A549	lung
20	chr6:13395400-13399400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:13395400-13399400	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr6:13395400-13399600	Enhancers	Left Ventricle	heart
23	chr6:13395600-13399400	Enhancers	Right Ventricle	heart
24	chr6:13395600-13402800	Enhancers	Fetal Heart	heart
25	chr6:13396000-13398200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:13396000-13398200	Enhancers	Colonic Mucosa	Colon
27	chr6:13396000-13398400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr6:13396000-13404400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr6:13396200-13398200	Enhancers	Hela-S3	cervix
30	chr6:13396200-13398400	Enhancers	HUVEC	blood vessel
31	chr6:13396200-13399400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:13396200-13407000	Weak transcription	Gastric	stomach
33	chr6:13396400-13404400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:13396600-13405800	Weak transcription	HepG2	liver
35	chr6:13396800-13398600	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr6:13396800-13404400	Weak transcription	NHLF	lung
37	chr6:13397000-13398800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr6:13397000-13399000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:13397000-13399000	Enhancers	HMEC	breast
40	chr6:13397000-13399400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:13397000-13404600	Weak transcription	Aorta	Aorta
42	chr6:13397200-13398200	Enhancers	Fetal Muscle Leg	muscle
43	chr6:13397200-13399200	Enhancers	HSMMtube	muscle
44	chr6:13397200-13399800	Enhancers	Brain Cingulate Gyrus	brain
45	chr6:13397200-13400000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:13397400-13398400	Weak transcription	Brain Angular Gyrus	brain
47	chr6:13397400-13398400	Weak transcription	Brain Anterior Caudate	brain
48	chr6:13397400-13398800	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr6:13397400-13398800	Weak transcription	Brain Substantia Nigra	brain
50	chr6:13397400-13398800	Enhancers	Fetal Muscle Trunk	muscle

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