Variant report

Variant	rs6685106
Chromosome Location	chr1:227436196-227436197
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10429872	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10495255	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10753433	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10799409	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10799410	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916106	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10916108	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916111	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10916118	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12035986	0.82[EUR][1000 genomes]
rs12044287	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12065126	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137591	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12565871	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12566059	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12569227	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12742066	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1913344	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2102638	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34084723	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34875093	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35738984	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3795457	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4339829	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4653797	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4653812	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60197034	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6656653	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6692294	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6697272	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6700730	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72759337	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7516326	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7519752	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7537038	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs955704	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227414000-227459200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:227414200-227453800	Weak transcription	HSMM	muscle
3	chr1:227415800-227456800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:227424800-227440800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:227425400-227445200	Weak transcription	Osteobl	bone
6	chr1:227431600-227486200	Weak transcription	NHDF-Ad	bronchial
7	chr1:227431800-227439200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:227431800-227443000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:227432000-227459200	Weak transcription	Fetal Lung	lung
10	chr1:227432200-227455400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:227432600-227436200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:227432600-227448000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:227432800-227441600	Weak transcription	Brain Angular Gyrus	brain
14	chr1:227432800-227442400	Weak transcription	K562	blood
15	chr1:227432800-227446000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:227432800-227455600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr1:227433000-227436600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:227433000-227438000	Weak transcription	Psoas Muscle	Psoas
19	chr1:227433000-227438400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:227433000-227441600	Weak transcription	A549	lung
21	chr1:227433000-227446000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:227433000-227446000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:227433000-227469000	Weak transcription	Aorta	Aorta
24	chr1:227433200-227452800	Weak transcription	Ovary	ovary
25	chr1:227434000-227442200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:227434000-227444200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:227434000-227446800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr1:227434000-227447000	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:227434000-227453400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:227434200-227440200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:227434200-227440600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:227434200-227442800	Weak transcription	Fetal Stomach	stomach
33	chr1:227434200-227455400	Weak transcription	Left Ventricle	heart
34	chr1:227434200-227455400	Weak transcription	Right Ventricle	heart
35	chr1:227434200-227455800	Weak transcription	Adipose Nuclei	Adipose
36	chr1:227434400-227442800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:227434400-227443400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:227434400-227446000	Weak transcription	Brain Substantia Nigra	brain
39	chr1:227434600-227468800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:227434800-227443000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:227434800-227458400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:227435000-227439000	Weak transcription	Fetal Brain Male	brain
43	chr1:227435000-227457000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:227435600-227436600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:227435600-227453600	Weak transcription	Fetal Intestine Small	intestine

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