Variant report

Variant	rs2179106
Chromosome Location	chr1:171190417-171190418
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10912616	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12065544	0.97[ASN][1000 genomes]
rs12402732	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12403890	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12720462	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16864174	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16864177	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16864194	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16864216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1987921	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1987944	1.00[ASN][1000 genomes]
rs2020863	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2049920	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2064077	0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2072755	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2075988	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2103537	0.82[ASN][1000 genomes]
rs28369845	0.83[EUR][1000 genomes]
rs28369881	0.83[EUR][1000 genomes]
rs28369891	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28369914	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3861947	0.97[ASN][1000 genomes]
rs4073692	0.84[ASN][1000 genomes]
rs4073693	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4622096	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4631734	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs56370691	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57305992	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61815361	0.83[EUR][1000 genomes]
rs61815363	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61815421	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61815423	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61815424	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61815425	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61815427	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714167	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535210	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7551934	0.96[AMR][1000 genomes];0.99[ASN][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	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats 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 miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv3493183	chr1:171189993-171190434	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171187800-171191400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:171188000-171192200	Weak transcription	Pancreas	Pancrea
3	chr1:171189000-171191000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:171189000-171191600	Weak transcription	Small Intestine	intestine
5	chr1:171189200-171190600	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr1:171189200-171192600	Enhancers	Muscle Satellite Cultured Cells	--
7	chr1:171189600-171190600	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr1:171189600-171191000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:171189600-171191200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:171189800-171193400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:171190000-171190800	Weak transcription	HSMMtube	muscle
12	chr1:171190000-171191000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:171190000-171191000	Weak transcription	Aorta	Aorta
14	chr1:171190000-171191000	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:171190000-171191000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr1:171190000-171191000	Weak transcription	Fetal Kidney	kidney
17	chr1:171190000-171191000	Weak transcription	Left Ventricle	heart
18	chr1:171190000-171192400	Enhancers	Osteobl	bone
19	chr1:171190000-171192600	Enhancers	HMEC	breast
20	chr1:171190200-171190600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr1:171190200-171190600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:171190200-171190600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:171190200-171190600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:171190200-171190600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:171190200-171190600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:171190200-171190600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:171190200-171190600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:171190200-171190600	Weak transcription	Fetal Intestine Large	intestine
29	chr1:171190200-171190600	Weak transcription	Placenta	Placenta
30	chr1:171190200-171190600	Weak transcription	Ovary	ovary
31	chr1:171190200-171190600	Weak transcription	Psoas Muscle	Psoas
32	chr1:171190200-171190600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr1:171190200-171190800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr1:171190200-171190800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr1:171190200-171190800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:171190200-171190800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr1:171190200-171190800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr1:171190200-171190800	Weak transcription	Fetal Stomach	stomach
39	chr1:171190200-171191000	Weak transcription	Fetal Intestine Small	intestine
40	chr1:171190200-171191000	Weak transcription	Right Atrium	heart
41	chr1:171190200-171191200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:171190200-171191200	Enhancers	Fetal Muscle Trunk	muscle
43	chr1:171190200-171191400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:171190200-171192000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:171190200-171192200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr1:171190200-171192200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr1:171190200-171192400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:171190200-171192400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:171190200-171192600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:171190200-171192600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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