Variant report

Variant	rs2172359
Chromosome Location	chr1:224327898-224327899
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10737430	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10737435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10737437	1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753448	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753453	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753455	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10799483	1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799486	1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916326	1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916328	1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes]
rs10916351	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10916388	0.92[ASW][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916472	1.00[JPT][hapmap]
rs11804140	0.91[ASW][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12239466	1.00[MEX][hapmap];0.82[MKK][hapmap]
rs13313058	1.00[ASN][1000 genomes]
rs1586888	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1602706	1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1810344	0.91[AFR][1000 genomes]
rs1891738	0.91[ASW][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1891739	1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2035897	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048994	0.92[ASW][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404844	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404845	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404846	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404847	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2896984	1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs2896986	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4353057	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653565	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4653955	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653956	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653985	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4653987	0.92[AFR][1000 genomes]
rs56718298	1.00[ASN][1000 genomes]
rs56887412	1.00[ASN][1000 genomes]
rs57138220	1.00[ASN][1000 genomes]
rs57746928	1.00[ASN][1000 genomes]
rs57823919	1.00[ASN][1000 genomes]
rs58090997	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59018039	1.00[ASN][1000 genomes]
rs59368039	1.00[ASN][1000 genomes]
rs59518883	1.00[ASN][1000 genomes]
rs59819476	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60013765	1.00[ASN][1000 genomes]
rs60381264	1.00[ASN][1000 genomes]
rs60432349	1.00[ASN][1000 genomes]
rs60643079	1.00[ASN][1000 genomes]
rs60972853	1.00[ASN][1000 genomes]
rs61074366	1.00[ASN][1000 genomes]
rs61144016	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61347348	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61495337	1.00[ASN][1000 genomes]
rs6426108	1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426112	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426135	0.91[AFR][1000 genomes]
rs6426144	0.80[AFR][1000 genomes]
rs6426162	1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6657160	0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6659249	1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663997	1.00[ASN][1000 genomes]
rs6668856	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668862	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670475	1.00[ASN][1000 genomes]
rs6670483	1.00[ASN][1000 genomes]
rs6670591	1.00[ASN][1000 genomes]
rs6671784	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679683	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687331	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689914	1.00[ASN][1000 genomes]
rs6689922	1.00[ASN][1000 genomes]
rs6690358	1.00[ASN][1000 genomes]
rs6690543	1.00[ASN][1000 genomes]
rs6702019	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704386	0.81[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73120501	1.00[ASN][1000 genomes]
rs73122403	1.00[ASN][1000 genomes]
rs73122404	1.00[ASN][1000 genomes]
rs73122411	1.00[ASN][1000 genomes]
rs73122413	1.00[ASN][1000 genomes]
rs73122436	1.00[ASN][1000 genomes]
rs73122438	1.00[ASN][1000 genomes]
rs73122441	1.00[ASN][1000 genomes]
rs73122446	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73124453	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73126416	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7526301	0.87[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7526876	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7535007	0.91[ASW][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537121	1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546034	1.00[MEX][hapmap]
rs908793	0.92[ASW][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs908796	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs937155	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs969008	1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs969009	1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv427941	chr1:224085052-224363163	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv873222	chr1:224292898-224335422	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224303000-224329000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:224303000-224363400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:224314400-224333800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:224314400-224343400	Weak transcription	Psoas Muscle	Psoas
5	chr1:224315800-224331200	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:224316400-224331200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr1:224316600-224352200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:224317200-224329800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:224317600-224328400	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:224317600-224333400	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:224317800-224328200	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr1:224317800-224328400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:224317800-224334000	Strong transcription	Fetal Intestine Large	intestine
14	chr1:224318000-224328400	Strong transcription	Primary B cells from peripheral blood	blood
15	chr1:224318000-224328400	Strong transcription	Fetal Thymus	thymus
16	chr1:224318000-224328600	Strong transcription	Duodenum Mucosa	Duodenum
17	chr1:224318000-224329600	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr1:224318000-224330600	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr1:224318000-224331200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:224318000-224332000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:224318200-224333400	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr1:224318400-224331200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:224319200-224329600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:224319200-224334000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:224319200-224335000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:224319400-224328200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:224319600-224328400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:224319800-224331200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:224320200-224344800	Weak transcription	Gastric	stomach
30	chr1:224320200-224345000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr1:224320200-224345000	Weak transcription	HUVEC	blood vessel
32	chr1:224320400-224329800	Weak transcription	Spleen	Spleen
33	chr1:224320400-224344800	Weak transcription	Small Intestine	intestine
34	chr1:224320400-224345000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:224320400-224345000	Weak transcription	Right Ventricle	heart
36	chr1:224320400-224345200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr1:224320600-224344000	Weak transcription	Brain Germinal Matrix	brain
38	chr1:224320600-224345000	Weak transcription	Pancreas	Pancrea
39	chr1:224320600-224345200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:224320800-224339000	Weak transcription	A549	lung
41	chr1:224320800-224343200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr1:224320800-224344200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr1:224320800-224344800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr1:224320800-224345200	Weak transcription	Brain Substantia Nigra	brain
45	chr1:224321000-224328200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:224321000-224329200	Weak transcription	Fetal Kidney	kidney
47	chr1:224321000-224329600	Weak transcription	Ovary	ovary
48	chr1:224321000-224337200	Weak transcription	Brain Hippocampus Middle	brain
49	chr1:224321000-224338400	Weak transcription	Brain Angular Gyrus	brain
50	chr1:224321000-224343200	Weak transcription	Colon Smooth Muscle	Colon

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