Variant report

Variant	rs662541
Chromosome Location	chr6:161413211-161413212
allele	A/C
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:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:158243442..158245618-chr6:161412032..161413556,2	K562	blood:
2	chr6:161411531..161413327-chr6:161653025..161655728,2	K562	blood:
3	chr6:161411809..161413437-chr6:161693885..161696604,2	K562	blood:
4	chr6:161349966..161354183-chr6:161410810..161413824,4	MCF-7	breast:
5	chr6:161412566..161414577-chr6:161651798..161653599,2	K562	blood:
6	chr6:161300742..161302528-chr6:161411919..161413550,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AGPAT4-1	chr6:161411350-161413374	ENSG00000272841.1

No data

Variant related genes	Relation type
ENSG00000231863	Chromatin interaction
ENSG00000026652	Chromatin interaction
ENSG00000130340	Chromatin interaction
ENSG00000224371	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1001809	0.89[AMR][1000 genomes]
rs4709486	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4709489	0.89[AMR][1000 genomes]
rs587501	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs615269	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs619393	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs628430	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs628923	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6455701	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs647923	0.83[EUR][1000 genomes]
rs655605	0.89[EUR][1000 genomes]
rs657551	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs668638	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs682110	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs683549	0.82[EUR][1000 genomes]
rs685388	0.81[EUR][1000 genomes]
rs6908283	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6913706	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6925502	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6929462	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs705829	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs705830	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7760056	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9346846	0.94[AMR][1000 genomes]
rs9355330	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422347	chr6:161211171-161442377	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1030045	chr6:161359075-161562255	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv886817	chr6:161371621-161846654	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv3381361	chr6:161373617-161864101	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1023982	chr6:161382188-161549831	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	esv3357609	chr6:161411812-161414260	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv3427182	chr6:161411987-161414535	Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161411200-161414000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:161411200-161414600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:161411600-161414000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr6:161411600-161414200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:161411600-161414400	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr6:161411800-161413400	Active TSS	Fetal Lung	lung
7	chr6:161411800-161414000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:161411800-161414000	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr6:161411800-161414000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:161411800-161414000	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr6:161411800-161414000	Active TSS	Brain Cingulate Gyrus	brain
12	chr6:161411800-161414000	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr6:161411800-161414000	Active TSS	Brain Substantia Nigra	brain
14	chr6:161411800-161414000	Active TSS	Fetal Intestine Large	intestine
15	chr6:161411800-161414000	Active TSS	Fetal Muscle Leg	muscle
16	chr6:161411800-161414000	Active TSS	K562	blood
17	chr6:161411800-161414000	Active TSS	NHLF	lung
18	chr6:161411800-161414200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:161411800-161414200	Active TSS	Brain Angular Gyrus	brain
20	chr6:161411800-161414200	Active TSS	Fetal Kidney	kidney
21	chr6:161411800-161414200	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr6:161411800-161414200	Active TSS	Rectal Smooth Muscle	rectum
23	chr6:161411800-161414200	Active TSS	HSMMtube	muscle
24	chr6:161411800-161414400	Active TSS	H1 Cell Line	embryonic stem cell
25	chr6:161411800-161414400	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr6:161411800-161414400	Active TSS	HMEC	breast
27	chr6:161411800-161414400	Active TSS	NH-A	brain
28	chr6:161411800-161417800	Active TSS	GM12878-XiMat	blood
29	chr6:161412000-161413400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:161412000-161413400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:161412000-161413400	Active TSS	Duodenum Mucosa	Duodenum
32	chr6:161412000-161413400	Active TSS	Placenta	Placenta
33	chr6:161412000-161413600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr6:161412000-161413600	Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr6:161412000-161413800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:161412000-161413800	Active TSS	Aorta	Aorta
37	chr6:161412000-161413800	Active TSS	Placenta Amnion	Placenta Amnion
38	chr6:161412000-161414000	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr6:161412000-161414000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr6:161412000-161414000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:161412000-161414000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr6:161412000-161414000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:161412000-161414000	Active TSS	Brain Anterior Caudate	brain
44	chr6:161412000-161414000	Active TSS	Brain Hippocampus Middle	brain
45	chr6:161412000-161414000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:161412000-161414000	Active TSS	Colon Smooth Muscle	Colon
47	chr6:161412000-161414000	Active TSS	Fetal Muscle Trunk	muscle
48	chr6:161412000-161414000	Active TSS	Rectal Mucosa Donor 31	rectum
49	chr6:161412000-161414000	Active TSS	Right Ventricle	heart
50	chr6:161412000-161414000	Active TSS	Hela-S3	cervix

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