Variant report

Variant	rs12064117
Chromosome Location	chr1:171190845-171190846
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10912525	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12066662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12067810	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12071595	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12072321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12078869	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12082112	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12086788	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12087971	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12091865	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13353034	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16864136	0.85[EUR][1000 genomes]
rs16864165	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16864191	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16864245	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2020860	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2020865	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2205726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28369826	0.90[EUR][1000 genomes]
rs28369834	0.90[EUR][1000 genomes]
rs28369837	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28369850	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28369868	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28369872	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28369883	0.90[EUR][1000 genomes]
rs28369886	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28969551	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs29001609	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56060753	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56159716	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56233063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57182460	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58324390	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58956470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59910498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61225278	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61233777	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6668231	0.91[EUR][1000 genomes]
rs6673781	0.91[EUR][1000 genomes]
rs6684218	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6689616	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73032526	0.91[EUR][1000 genomes]
rs74122287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7527107	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

No data

Chromatin state (count:71 , 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	chr1:171189200-171192600	Enhancers	Muscle Satellite Cultured Cells	--
6	chr1:171189600-171191000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:171189600-171191200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:171189800-171193400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:171190000-171191000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:171190000-171191000	Weak transcription	Aorta	Aorta
11	chr1:171190000-171191000	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:171190000-171191000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:171190000-171191000	Weak transcription	Fetal Kidney	kidney
14	chr1:171190000-171191000	Weak transcription	Left Ventricle	heart
15	chr1:171190000-171192400	Enhancers	Osteobl	bone
16	chr1:171190000-171192600	Enhancers	HMEC	breast
17	chr1:171190200-171191000	Weak transcription	Fetal Intestine Small	intestine
18	chr1:171190200-171191000	Weak transcription	Right Atrium	heart
19	chr1:171190200-171191200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:171190200-171191200	Enhancers	Fetal Muscle Trunk	muscle
21	chr1:171190200-171191400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:171190200-171192000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:171190200-171192200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:171190200-171192200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:171190200-171192400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:171190200-171192400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:171190200-171192600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:171190200-171192600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:171190200-171192600	Enhancers	Fetal Muscle Leg	muscle
30	chr1:171190200-171192600	Enhancers	NHLF	lung
31	chr1:171190200-171192800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:171190200-171193200	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr1:171190200-171193400	Enhancers	NHEK	skin
34	chr1:171190200-171193800	Enhancers	Fetal Lung	lung
35	chr1:171190400-171191000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:171190400-171193800	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr1:171190600-171191000	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr1:171190600-171191000	Enhancers	Psoas Muscle	Psoas
39	chr1:171190600-171191200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:171190600-171191200	Enhancers	Ovary	ovary
41	chr1:171190600-171191400	Enhancers	Fetal Intestine Large	intestine
42	chr1:171190600-171191600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:171190600-171191600	Enhancers	NH-A	brain
44	chr1:171190600-171191800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:171190600-171191800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:171190600-171191800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr1:171190600-171192200	Enhancers	Stomach Smooth Muscle	stomach
48	chr1:171190600-171192400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:171190600-171192400	Enhancers	Placenta	Placenta
50	chr1:171190600-171192400	Enhancers	NHDF-Ad	bronchial

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