Variant report

Variant	rs12407061
Chromosome Location	chr1:227288049-227288050
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 133 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10495258	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10495263	1.00[CEU][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10495266	0.98[EUR][1000 genomes]
rs10495269	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10495270	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11799413	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11800062	0.93[EUR][1000 genomes]
rs11801443	0.94[EUR][1000 genomes]
rs11802395	0.98[EUR][1000 genomes]
rs11803761	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11803959	0.94[EUR][1000 genomes]
rs11805298	0.82[EUR][1000 genomes]
rs11806820	0.98[EUR][1000 genomes]
rs11806937	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11808186	0.98[EUR][1000 genomes]
rs11809998	0.95[EUR][1000 genomes]
rs12401556	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12401963	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12403195	0.95[EUR][1000 genomes]
rs12403391	0.98[EUR][1000 genomes]
rs12403833	0.91[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12404494	0.98[EUR][1000 genomes]
rs12404627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12405122	0.94[EUR][1000 genomes]
rs12405686	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12405707	0.93[EUR][1000 genomes]
rs12405723	0.88[EUR][1000 genomes]
rs12405878	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12407545	0.95[EUR][1000 genomes]
rs12408437	0.98[EUR][1000 genomes]
rs12408913	0.80[AMR][1000 genomes]
rs12409816	0.92[EUR][1000 genomes]
rs12410327	1.00[CEU][hapmap];0.80[AMR][1000 genomes]
rs12410337	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12410460	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12411017	0.96[EUR][1000 genomes]
rs1320493	0.96[EUR][1000 genomes]
rs1464076	0.80[AMR][1000 genomes]
rs1464077	1.00[CEU][hapmap]
rs1513600	0.98[EUR][1000 genomes]
rs1513603	0.82[EUR][1000 genomes]
rs1606549	0.80[AMR][1000 genomes]
rs16846855	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs16846874	0.98[EUR][1000 genomes]
rs16846877	0.98[EUR][1000 genomes]
rs16846908	0.98[EUR][1000 genomes]
rs16846910	0.98[EUR][1000 genomes]
rs16846911	0.98[EUR][1000 genomes]
rs16846972	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs16846985	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs16847014	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs16847035	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs16847098	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs16847107	1.00[CEU][hapmap]
rs16847492	1.00[CEU][hapmap]
rs17605533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17851754	0.98[EUR][1000 genomes]
rs1877622	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1888831	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2090009	0.98[EUR][1000 genomes]
rs2150869	0.96[EUR][1000 genomes]
rs2150871	0.93[EUR][1000 genomes]
rs2150873	0.98[EUR][1000 genomes]
rs2183837	0.98[EUR][1000 genomes]
rs34263105	0.86[AMR][1000 genomes]
rs34400564	0.82[EUR][1000 genomes]
rs34953255	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41303115	0.98[EUR][1000 genomes]
rs4551563	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55685166	0.98[EUR][1000 genomes]
rs55865118	0.98[EUR][1000 genomes]
rs56834719	0.95[EUR][1000 genomes]
rs57513303	0.98[EUR][1000 genomes]
rs58532064	0.98[EUR][1000 genomes]
rs59116340	0.82[EUR][1000 genomes]
rs60079575	0.94[EUR][1000 genomes]
rs60291100	0.98[EUR][1000 genomes]
rs60641481	0.98[EUR][1000 genomes]
rs60866629	0.95[EUR][1000 genomes]
rs60979561	0.98[EUR][1000 genomes]
rs61522132	0.82[EUR][1000 genomes]
rs6675383	0.88[EUR][1000 genomes]
rs6696791	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6696794	0.98[EUR][1000 genomes]
rs6701743	0.95[EUR][1000 genomes]
rs73086746	0.93[EUR][1000 genomes]
rs73086752	0.93[EUR][1000 genomes]
rs73086775	0.93[EUR][1000 genomes]
rs73088658	0.82[EUR][1000 genomes]
rs73089725	0.95[EUR][1000 genomes]
rs73089747	0.95[EUR][1000 genomes]
rs73089755	0.98[EUR][1000 genomes]
rs73089760	0.98[EUR][1000 genomes]
rs73089765	0.98[EUR][1000 genomes]
rs73089770	0.98[EUR][1000 genomes]
rs73090612	0.82[EUR][1000 genomes]
rs73091738	0.98[EUR][1000 genomes]
rs73091740	0.98[EUR][1000 genomes]
rs73091742	0.98[EUR][1000 genomes]
rs73091755	0.98[EUR][1000 genomes]
rs73091759	0.98[EUR][1000 genomes]
rs73091761	0.98[EUR][1000 genomes]
rs73091774	0.98[EUR][1000 genomes]
rs73093463	0.96[EUR][1000 genomes]
rs73093495	0.96[EUR][1000 genomes]
rs73099023	0.98[EUR][1000 genomes]
rs73099026	0.98[EUR][1000 genomes]
rs73100804	0.98[EUR][1000 genomes]
rs73100814	0.98[EUR][1000 genomes]
rs73100852	0.96[EUR][1000 genomes]
rs73102915	0.96[EUR][1000 genomes]
rs73102920	0.95[EUR][1000 genomes]
rs73102930	0.95[EUR][1000 genomes]
rs73102936	0.95[EUR][1000 genomes]
rs7413768	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs74140276	0.96[EUR][1000 genomes]
rs74143321	0.92[EUR][1000 genomes]
rs7526283	1.00[CEU][hapmap]
rs7534286	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7535010	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7539037	0.82[EUR][1000 genomes]
rs7539750	0.82[EUR][1000 genomes]
rs7542505	1.00[CEU][hapmap]
rs7551556	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
2	chr1:227209200-227301600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:227214800-227329200	Weak transcription	Right Ventricle	heart
4	chr1:227247400-227299800	Weak transcription	HMEC	breast
5	chr1:227251000-227300000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:227257800-227312200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:227259400-227349000	Weak transcription	Colonic Mucosa	Colon
8	chr1:227271800-227299600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:227272600-227294400	Weak transcription	Fetal Heart	heart
10	chr1:227272800-227295000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:227272800-227295000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:227272800-227331000	Weak transcription	Lung	lung
13	chr1:227273000-227312400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:227275800-227302600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr1:227277000-227288600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:227277200-227302600	Weak transcription	Brain Substantia Nigra	brain
17	chr1:227279800-227299000	Weak transcription	Placenta	Placenta
18	chr1:227280800-227298800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:227281800-227294400	Weak transcription	Fetal Kidney	kidney
20	chr1:227282600-227318000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:227283800-227288600	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:227284000-227288800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:227284400-227288600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:227284800-227288600	Strong transcription	Brain Hippocampus Middle	brain
25	chr1:227285000-227288600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:227285200-227288200	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:227285200-227288600	Strong transcription	Fetal Brain Female	brain
28	chr1:227285200-227288600	Strong transcription	Fetal Muscle Trunk	muscle
29	chr1:227285200-227288600	Strong transcription	Fetal Muscle Leg	muscle
30	chr1:227285200-227289000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:227285400-227288600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:227285400-227288600	Strong transcription	Skeletal Muscle Female	skeletal muscle
33	chr1:227285400-227288800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:227285600-227288600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:227285600-227288600	Strong transcription	Left Ventricle	heart
36	chr1:227285600-227288800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:227285600-227297600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr1:227285600-227308600	Weak transcription	Pancreas	Pancrea
39	chr1:227285600-227313800	Weak transcription	Gastric	stomach
40	chr1:227285800-227288400	Weak transcription	Stomach Mucosa	stomach
41	chr1:227285800-227288600	Strong transcription	K562	blood
42	chr1:227286000-227288200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:227286000-227288800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:227286000-227288800	Strong transcription	Adipose Nuclei	Adipose
45	chr1:227286200-227288600	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr1:227286200-227288600	Strong transcription	Stomach Smooth Muscle	stomach
47	chr1:227286200-227288800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:227286200-227290200	Strong transcription	HUVEC	blood vessel
49	chr1:227286400-227288200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:227286400-227288400	Strong transcription	Ovary	ovary

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