Variant report

Variant	rs1546143
Chromosome Location	chr1:247161527-247161528
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1018048	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737797	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10754535	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10802455	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10802456	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10802457	1.00[JPT][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes]
rs10802458	1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10802460	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10802461	1.00[ASN][1000 genomes]
rs10924879	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10924887	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12030877	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12045053	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12048616	1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12048664	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12057312	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12119510	1.00[JPT][hapmap]
rs12405787	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12563635	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1691228	1.00[JPT][hapmap]
rs1874200	1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453405	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453407	0.81[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2642956	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2642973	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2642992	0.80[CEU][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2642993	1.00[JPT][hapmap]
rs2642995	0.80[CEU][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2818876	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3104110	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3749427	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4384270	1.00[JPT][hapmap]
rs4506496	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4971301	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4971306	1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4971310	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61852611	0.92[ASN][1000 genomes]
rs6426194	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6668864	1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678796	1.00[ASN][1000 genomes]
rs6694946	1.00[JPT][hapmap];0.80[TSI][hapmap]
rs6698318	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6702728	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7513728	0.81[CEU][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516037	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7519943	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7544897	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555643	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv1000602	chr1:247044627-247226568	Enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv873426	chr1:247069514-247162628	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv535417	chr1:247094131-247409000	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
9	nsv1005639	chr1:247094161-247401380	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
10	nsv535418	chr1:247094161-247401380	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
11	nsv524007	chr1:247098587-247162658	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv1002054	chr1:247108896-247161897	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv535419	chr1:247108896-247161897	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv999879	chr1:247112207-247276918	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
15	nsv916236	chr1:247124353-247409065	Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
16	nsv948419	chr1:247130577-247400404	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
17	nsv873427	chr1:247140425-247218227	ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
18	nsv549546	chr1:247145690-247205056	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247136600-247161600	ZNF genes & repeats	Dnd41	blood
2	chr1:247136600-247164600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:247140600-247163400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:247140800-247162800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
5	chr1:247144200-247163600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:247150200-247162000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:247151200-247170800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:247151600-247170000	Weak transcription	Osteobl	bone
9	chr1:247155200-247168800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:247155800-247163200	ZNF genes & repeats	Fetal Brain Female	brain
11	chr1:247156200-247163400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:247156400-247163200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr1:247157800-247161800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:247158000-247170200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:247158200-247163400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
16	chr1:247158400-247163200	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:247158400-247163600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
18	chr1:247158400-247164400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:247158400-247167800	Weak transcription	HUVEC	blood vessel
20	chr1:247158600-247163400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
21	chr1:247158600-247164200	Weak transcription	Small Intestine	intestine
22	chr1:247159000-247162400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr1:247159000-247163400	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr1:247159200-247165800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:247159600-247161800	Weak transcription	Fetal Stomach	stomach
26	chr1:247159600-247162000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:247159600-247162400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:247159600-247164200	Weak transcription	HepG2	liver
29	chr1:247159600-247170000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:247159800-247162600	Weak transcription	Thymus	Thymus
31	chr1:247159800-247163400	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr1:247159800-247163400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:247159800-247166200	Weak transcription	Hela-S3	cervix
34	chr1:247160000-247161600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
35	chr1:247160200-247163400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:247160400-247162400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:247160600-247161800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:247160600-247162000	Strong transcription	HSMM	muscle
39	chr1:247160600-247163000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:247160600-247163400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:247160800-247162200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:247160800-247162400	Strong transcription	Fetal Lung	lung
43	chr1:247160800-247164600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
44	chr1:247161000-247161600	ZNF genes & repeats	K562	blood
45	chr1:247161000-247161800	ZNF genes & repeats	ES-WA7 Cell Line	embryonic stem cell
46	chr1:247161000-247161800	Weak transcription	Fetal Thymus	thymus
47	chr1:247161000-247163400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:247161200-247162600	Strong transcription	Brain Germinal Matrix	brain
49	chr1:247161200-247163800	Weak transcription	Duodenum Mucosa	Duodenum
50	chr1:247161200-247164400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell

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