Variant report

Variant	rs488104
Chromosome Location	chr1:227300277-227300278
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10799381	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916080	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12039370	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12139758	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1320494	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1483	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1929858	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2102634	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2482454	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2492630	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2670462	0.83[AMR][1000 genomes]
rs2670471	0.80[AMR][1000 genomes]
rs2813950	0.80[AMR][1000 genomes]
rs2813965	0.80[AMR][1000 genomes]
rs2813969	0.80[AMR][1000 genomes]
rs2813970	0.80[AMR][1000 genomes]
rs3754418	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4351610	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4653479	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485234	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs498020	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56219094	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs648877	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662583	0.85[AMR][1000 genomes]
rs6682472	0.83[AMR][1000 genomes]
rs6682642	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685823	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692080	0.83[AMR][1000 genomes]
rs6699828	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs689094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs694740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7412928	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7521110	0.85[AMR][1000 genomes]
rs7521639	1.00[ASN][1000 genomes]
rs7523167	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7543579	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7549520	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1011654	chr1:227196502-227308416	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv832792	chr1:227211378-227364992	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv873239	chr1:227222125-227361072	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv468227	chr1:227223736-227340790	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv549269	chr1:227223736-227340790	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv873240	chr1:227228946-227361072	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv873241	chr1:227242247-227361072	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv522990	chr1:227290139-227302912	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv549270	chr1:227290139-227361072	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	esv2830098	chr1:227295716-227422234	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227209200-227301600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:227214800-227329200	Weak transcription	Right Ventricle	heart
3	chr1:227257800-227312200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:227259400-227349000	Weak transcription	Colonic Mucosa	Colon
5	chr1:227272800-227331000	Weak transcription	Lung	lung
6	chr1:227273000-227312400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:227275800-227302600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:227277200-227302600	Weak transcription	Brain Substantia Nigra	brain
9	chr1:227282600-227318000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:227285600-227308600	Weak transcription	Pancreas	Pancrea
11	chr1:227285600-227313800	Weak transcription	Gastric	stomach
12	chr1:227286400-227328200	Weak transcription	Brain Germinal Matrix	brain
13	chr1:227287400-227360800	Weak transcription	Psoas Muscle	Psoas
14	chr1:227288000-227326400	Weak transcription	A549	lung
15	chr1:227288200-227332400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:227288400-227302200	Weak transcription	Fetal Brain Male	brain
17	chr1:227288400-227343000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:227288400-227398000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:227288600-227310800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:227288600-227312200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:227288600-227313000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr1:227288600-227316000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr1:227288600-227328200	Weak transcription	Fetal Stomach	stomach
24	chr1:227288600-227332400	Weak transcription	NHLF	lung
25	chr1:227288600-227333600	Weak transcription	Esophagus	oesophagus
26	chr1:227288800-227317200	Weak transcription	NHEK	skin
27	chr1:227288800-227330000	Weak transcription	NHDF-Ad	bronchial
28	chr1:227289000-227312000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr1:227290200-227309800	Weak transcription	Fetal Intestine Small	intestine
30	chr1:227294600-227300600	Strong transcription	HSMM	muscle
31	chr1:227295200-227301200	Weak transcription	Fetal Heart	heart
32	chr1:227295200-227316000	Weak transcription	Fetal Kidney	kidney
33	chr1:227295200-227346400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:227295400-227301200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:227295400-227310800	Weak transcription	Brain Angular Gyrus	brain
36	chr1:227295400-227313800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:227296000-227310600	Weak transcription	Small Intestine	intestine
38	chr1:227296400-227326200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:227296600-227316400	Weak transcription	HSMMtube	muscle
40	chr1:227296600-227326200	Weak transcription	Fetal Lung	lung
41	chr1:227297600-227300600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:227298600-227351800	Weak transcription	Hela-S3	cervix
43	chr1:227298800-227300600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:227299000-227300600	Strong transcription	Placenta	Placenta
45	chr1:227299200-227300600	Strong transcription	Left Ventricle	heart
46	chr1:227299200-227300600	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr1:227299200-227318800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:227299400-227300600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:227299400-227300600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:227299400-227300600	Strong transcription	Duodenum Mucosa	Duodenum

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