Variant report

Variant	rs1606549
Chromosome Location	chr1:227436880-227436881
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1015815	0.94[EUR][1000 genomes]
rs1015816	0.92[EUR][1000 genomes]
rs10495258	0.80[AMR][1000 genomes]
rs10495263	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs10916109	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10916114	0.95[EUR][1000 genomes]
rs11799413	1.00[CEU][hapmap]
rs11800062	0.81[EUR][1000 genomes]
rs11801994	0.96[EUR][1000 genomes]
rs11803590	0.96[EUR][1000 genomes]
rs11803761	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11805298	0.92[EUR][1000 genomes]
rs11806511	0.92[EUR][1000 genomes]
rs11806937	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11808928	0.96[EUR][1000 genomes]
rs11810328	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11811358	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12402456	0.96[EUR][1000 genomes]
rs12403650	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12403833	0.91[CEU][hapmap];0.80[AMR][1000 genomes]
rs12403986	0.96[EUR][1000 genomes]
rs12404627	0.80[AMR][1000 genomes]
rs12405363	0.93[EUR][1000 genomes]
rs12405878	1.00[CEU][hapmap]
rs12407061	0.80[AMR][1000 genomes]
rs12408913	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12410327	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12410337	1.00[CEU][hapmap]
rs12410460	1.00[CEU][hapmap]
rs12741049	0.87[EUR][1000 genomes]
rs1464076	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1464077	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1513602	0.96[EUR][1000 genomes]
rs1513603	0.92[EUR][1000 genomes]
rs1546557	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16846972	1.00[CEU][hapmap]
rs16846985	1.00[CEU][hapmap]
rs16847014	1.00[CEU][hapmap]
rs16847035	1.00[CEU][hapmap]
rs16847098	1.00[CEU][hapmap]
rs16847107	1.00[CEU][hapmap]
rs16847492	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs16847634	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs17605533	0.80[AMR][1000 genomes]
rs17613166	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1877622	1.00[CEU][hapmap]
rs1888831	1.00[CEU][hapmap]
rs34263105	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34400564	0.92[EUR][1000 genomes]
rs34953255	0.86[AMR][1000 genomes]
rs41270149	0.96[EUR][1000 genomes]
rs4255349	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4282782	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4300186	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4354510	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4434814	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4437846	0.94[EUR][1000 genomes]
rs4518864	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4543764	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4551563	0.80[AMR][1000 genomes]
rs55805110	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55882852	0.94[EUR][1000 genomes]
rs55946024	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57276421	0.96[EUR][1000 genomes]
rs57758974	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58489467	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59116340	0.92[EUR][1000 genomes]
rs59121440	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59859849	0.96[EUR][1000 genomes]
rs60068245	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60235610	0.96[EUR][1000 genomes]
rs60742095	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60958272	0.98[EUR][1000 genomes]
rs61081394	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61522132	0.92[EUR][1000 genomes]
rs6659506	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6668367	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6675521	1.00[YRI][hapmap]
rs73086746	0.81[EUR][1000 genomes]
rs73086752	0.81[EUR][1000 genomes]
rs73086775	0.81[EUR][1000 genomes]
rs73088658	0.92[EUR][1000 genomes]
rs73090612	0.92[EUR][1000 genomes]
rs73094351	0.94[EUR][1000 genomes]
rs73094393	0.96[EUR][1000 genomes]
rs73094400	0.98[EUR][1000 genomes]
rs73096317	0.98[EUR][1000 genomes]
rs73096350	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73096353	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73096358	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73096374	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73098390	0.93[EUR][1000 genomes]
rs73098398	0.93[EUR][1000 genomes]
rs73102307	0.93[EUR][1000 genomes]
rs7413768	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs74140153	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7515739	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7519099	0.95[EUR][1000 genomes]
rs7526283	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7534286	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7535010	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7539037	0.92[EUR][1000 genomes]
rs7539750	0.92[EUR][1000 genomes]
rs7542505	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7544923	0.95[EUR][1000 genomes]
rs7545775	0.98[EUR][1000 genomes]
rs7551556	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][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	chr1:227432600-227448000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:227432800-227441600	Weak transcription	Brain Angular Gyrus	brain
13	chr1:227432800-227442400	Weak transcription	K562	blood
14	chr1:227432800-227446000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:227432800-227455600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr1:227433000-227438000	Weak transcription	Psoas Muscle	Psoas
17	chr1:227433000-227438400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:227433000-227441600	Weak transcription	A549	lung
19	chr1:227433000-227446000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:227433000-227446000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:227433000-227469000	Weak transcription	Aorta	Aorta
22	chr1:227433200-227452800	Weak transcription	Ovary	ovary
23	chr1:227434000-227442200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:227434000-227444200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:227434000-227446800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr1:227434000-227447000	Weak transcription	Brain Hippocampus Middle	brain
27	chr1:227434000-227453400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:227434200-227440200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:227434200-227440600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:227434200-227442800	Weak transcription	Fetal Stomach	stomach
31	chr1:227434200-227455400	Weak transcription	Left Ventricle	heart
32	chr1:227434200-227455400	Weak transcription	Right Ventricle	heart
33	chr1:227434200-227455800	Weak transcription	Adipose Nuclei	Adipose
34	chr1:227434400-227442800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:227434400-227443400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:227434400-227446000	Weak transcription	Brain Substantia Nigra	brain
37	chr1:227434600-227468800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:227434800-227443000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:227434800-227458400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:227435000-227439000	Weak transcription	Fetal Brain Male	brain
41	chr1:227435000-227457000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:227435600-227453600	Weak transcription	Fetal Intestine Small	intestine
43	chr1:227436600-227437400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:227436600-227437800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:227436800-227440600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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