Variant report

Variant	rs16847487
Chromosome Location	chr1:165567970-165567971
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:165567791..165570618-chr1:165797003..165798586,2	K562	blood:
2	chr1:165564921..165568209-chr1:165795710..165798284,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MGST3-1	chr1:165567006-165569013	NONHSAT007321

Variant related genes	Relation type
ENSG00000143179	Chromatin interaction
ENSG00000143183	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10800127	1.00[CHB][hapmap]
rs11506	1.00[CHB][hapmap]
rs11799886	1.00[JPT][hapmap]
rs11799903	1.00[JPT][hapmap]
rs11800476	1.00[CHB][hapmap]
rs11801044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11801981	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11802672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11803276	1.00[ASN][1000 genomes]
rs11806754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16847544	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs57256442	0.89[ASN][1000 genomes]
rs58045866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59033716	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61557603	0.89[ASN][1000 genomes]
rs61804068	0.89[ASN][1000 genomes]
rs61804069	0.89[ASN][1000 genomes]
rs6666914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6682771	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6686643	1.00[JPT][hapmap]
rs6693448	1.00[JPT][hapmap]
rs6695758	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs72696026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72696027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72696028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72696029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516587	1.00[JPT][hapmap]
rs7550682	0.89[ASN][1000 genomes]
rs7554034	1.00[JPT][hapmap]
rs9333378	1.00[JPT][hapmap]
rs9333464	1.00[JPT][hapmap]
rs9333471	1.00[JPT][hapmap]
rs959617	1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429902	chr1:165531342-165574342	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165566600-165568000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr1:165566600-165568000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:165566800-165568000	Active TSS	H9 Cell Line	embryonic stem cell
4	chr1:165566800-165568000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
5	chr1:165566800-165568000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr1:165566800-165568000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:165566800-165568000	Active TSS	Colonic Mucosa	Colon
8	chr1:165566800-165568000	Active TSS	Fetal Brain Male	brain
9	chr1:165566800-165568200	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr1:165566800-165568200	Active TSS	H1 Cell Line	embryonic stem cell
11	chr1:165566800-165568200	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr1:165566800-165568200	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr1:165566800-165568200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr1:165566800-165568200	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr1:165566800-165568200	Flanking Active TSS	Dnd41	blood
16	chr1:165566800-165568200	Flanking Active TSS	K562	blood
17	chr1:165566800-165568600	Active TSS	Brain Germinal Matrix	brain
18	chr1:165567000-165568000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr1:165567000-165568000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:165567000-165568000	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr1:165567000-165568000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
22	chr1:165567000-165568000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
23	chr1:165567000-165568000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr1:165567000-165568000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:165567000-165568000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:165567000-165568000	Active TSS	Brain Hippocampus Middle	brain
27	chr1:165567000-165568000	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr1:165567000-165568000	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr1:165567000-165568000	Active TSS	Fetal Intestine Large	intestine
30	chr1:165567000-165568000	Active TSS	Fetal Kidney	kidney
31	chr1:165567000-165568000	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr1:165567000-165568000	Active TSS	Fetal Muscle Trunk	muscle
33	chr1:165567000-165568000	Flanking Active TSS	Placenta	Placenta
34	chr1:165567000-165568000	Active TSS	Psoas Muscle	Psoas
35	chr1:165567000-165568000	Active TSS	Right Atrium	heart
36	chr1:165567000-165568000	Active TSS	Right Ventricle	heart
37	chr1:165567000-165568200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:165567000-165568200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:165567000-165568200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:165567000-165568200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:165567000-165568200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:165567000-165568200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:165567000-165568200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:165567000-165568200	Flanking Active TSS	Liver	Liver
45	chr1:165567000-165568200	Active TSS	A549	lung
46	chr1:165567000-165568400	Active TSS	Fetal Brain Female	brain
47	chr1:165567200-165568000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr1:165567200-165568000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:165567200-165568000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:165567200-165568000	Active TSS	iPS-15b Cell Line	embryonic stem cell

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