Variant report

Variant	rs2093609
Chromosome Location	chr1:227820983-227820984
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 115 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10047205	0.91[JPT][hapmap]
rs1021553	1.00[CEU][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1021554	1.00[CEU][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10495276	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10799423	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10799431	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799432	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10799433	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799434	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799435	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916158	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10916159	0.87[EUR][1000 genomes]
rs10916165	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10916169	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10916175	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916176	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10916178	0.87[JPT][hapmap]
rs10916179	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916182	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916183	1.00[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916184	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916185	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916187	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11484723	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11580570	0.88[EUR][1000 genomes]
rs12023298	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12025815	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12040302	0.87[EUR][1000 genomes]
rs12070002	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070036	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079123	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12080321	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12080590	0.87[JPT][hapmap]
rs12082414	0.87[JPT][hapmap]
rs12096675	0.87[JPT][hapmap]
rs12132444	1.00[CEU][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12740317	0.84[EUR][1000 genomes]
rs1407718	1.00[CEU][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1495842	0.88[EUR][1000 genomes]
rs1495845	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1495847	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1495849	0.87[JPT][hapmap]
rs16847966	0.87[JPT][hapmap]
rs16847991	0.87[JPT][hapmap]
rs16847992	0.87[JPT][hapmap]
rs16848029	0.87[JPT][hapmap]
rs1845758	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2018401	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2088210	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2088211	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2088212	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2088214	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2093610	0.96[CEU][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2132366	0.87[JPT][hapmap]
rs2132367	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2201571	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2453682	0.83[JPT][hapmap]
rs2644140	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2644161	0.83[JPT][hapmap]
rs28407112	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2935145	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2935146	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2935147	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2935152	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2935155	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2999741	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999743	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2999744	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2999745	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2999746	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3010183	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3010186	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3010190	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3010191	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3010192	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3010193	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3010194	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3010195	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3010196	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3748806	0.91[JPT][hapmap]
rs4359006	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4376731	0.91[JPT][hapmap]
rs4653512	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4653514	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4653515	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4653848	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4653849	1.00[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4653850	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4653853	1.00[CEU][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6664682	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671825	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6683151	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6697867	1.00[CEU][hapmap];0.96[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7512348	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7523915	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7528094	1.00[CEU][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7539151	0.91[JPT][hapmap]
rs7539914	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7542685	0.82[EUR][1000 genomes]
rs7551459	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs903683	0.88[EUR][1000 genomes]
rs903684	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs903690	1.00[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs903694	0.87[JPT][hapmap]
rs903695	0.87[JPT][hapmap]
rs903697	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs951083	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs965942	0.87[JPT][hapmap]
rs976959	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	esv3327012	chr1:227741102-227890968	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv945342	chr1:227819395-227829907	ZNF genes & repeats Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227770000-227853800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:227790400-227834800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:227801200-227821800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:227805800-227823600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:227811800-227830600	ZNF genes & repeats	Liver	Liver
6	chr1:227815200-227828800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:227817400-227821200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
8	chr1:227818600-227822200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
9	chr1:227818600-227822600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:227818600-227830600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
11	chr1:227818600-227834200	ZNF genes & repeats	Fetal Brain Female	brain
12	chr1:227818800-227822800	ZNF genes & repeats	Primary B cells from cord blood	blood
13	chr1:227819000-227822400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:227819400-227823800	ZNF genes & repeats	Fetal Muscle Leg	muscle
15	chr1:227819800-227822000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
16	chr1:227819800-227825200	ZNF genes & repeats	Aorta	Aorta
17	chr1:227819800-227837600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:227820000-227821000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
19	chr1:227820000-227822000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:227820000-227822200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:227820000-227822800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:227820000-227822800	ZNF genes & repeats	Lung	lung
23	chr1:227820000-227823600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
24	chr1:227820000-227823800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
25	chr1:227820000-227823800	ZNF genes & repeats	Fetal Intestine Small	intestine
26	chr1:227820000-227829200	ZNF genes & repeats	Fetal Stomach	stomach
27	chr1:227820200-227821000	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
28	chr1:227820200-227821000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
29	chr1:227820200-227821000	ZNF genes & repeats	Fetal Intestine Large	intestine
30	chr1:227820200-227821400	Weak transcription	Colonic Mucosa	Colon
31	chr1:227820200-227822600	ZNF genes & repeats	Brain Germinal Matrix	brain
32	chr1:227820200-227830400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
33	chr1:227820200-227831400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
34	chr1:227820400-227821000	ZNF genes & repeats	Dnd41	blood
35	chr1:227820400-227824400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:227820600-227821400	Weak transcription	Fetal Lung	lung
37	chr1:227820600-227821600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:227820600-227822000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:227820600-227822000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
40	chr1:227820600-227822400	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr1:227820600-227822600	ZNF genes & repeats	Brain Hippocampus Middle	brain
42	chr1:227820600-227822600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
43	chr1:227820600-227822600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
44	chr1:227820600-227823000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
45	chr1:227820600-227825200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
46	chr1:227820600-227861600	ZNF genes & repeats	Adipose Nuclei	Adipose
47	chr1:227820800-227821000	ZNF genes & repeats	Ovary	ovary
48	chr1:227820800-227821600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
49	chr1:227820800-227821800	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
50	chr1:227820800-227822400	ZNF genes & repeats	Left Ventricle	heart

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