Variant report

Variant	rs12561922
Chromosome Location	chr1:169265794-169265795
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10047168	0.97[EUR][1000 genomes]
rs10800418	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10800430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800436	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs10800443	0.94[EUR][1000 genomes]
rs10800445	0.88[EUR][1000 genomes]
rs10919073	1.00[CEU][hapmap]
rs10919079	1.00[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap]
rs10919100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10919110	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10919131	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes]
rs10919152	0.94[EUR][1000 genomes]
rs10919156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes]
rs10919157	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs10919159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs1138486	1.00[CEU][hapmap]
rs11487548	0.88[EUR][1000 genomes]
rs11802239	1.00[CEU][hapmap]
rs11805562	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11806445	0.85[AFR][1000 genomes]
rs11807896	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11810815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes]
rs12058325	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12059944	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs12060959	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12061069	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12061080	0.97[EUR][1000 genomes]
rs12062884	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12063056	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12063719	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12063863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12065030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12067139	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12067351	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12071122	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12071224	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12071630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12073439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12074013	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap]
rs12074492	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12076519	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079745	1.00[CEU][hapmap]
rs12080100	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12081030	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12082748	1.00[CEU][hapmap]
rs12083249	1.00[CEU][hapmap]
rs12088672	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12089602	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12091133	0.88[EUR][1000 genomes]
rs12091844	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs12092506	0.88[EUR][1000 genomes]
rs12092952	0.88[EUR][1000 genomes]
rs12094791	0.88[EUR][1000 genomes]
rs12097260	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12097682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes]
rs12565852	0.88[EUR][1000 genomes]
rs12740226	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1591734	0.82[ASN][1000 genomes]
rs2275300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes]
rs2280257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs2982468	0.83[CHD][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs35144581	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3737683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3753298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3765227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3766052	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap]
rs3766064	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap]
rs3766077	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3766082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap]
rs3766088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766092	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs41272453	0.88[EUR][1000 genomes]
rs57776592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60011235	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61806984	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7515326	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7544446	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9628661	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv429913	chr1:169177019-169296744	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1012919	chr1:169200982-169324750	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1000254	chr1:169203554-169271792	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1009170	chr1:169207940-169270995	Weak transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv508637	chr1:169214920-169268078	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1004674	chr1:169233962-169271792	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169251400-169271400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:169252800-169278600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr1:169252800-169278800	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr1:169253400-169270800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:169253600-169280600	Weak transcription	Fetal Kidney	kidney
6	chr1:169254000-169274800	Weak transcription	Ovary	ovary
7	chr1:169254800-169268600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:169254800-169281000	Weak transcription	Dnd41	blood
9	chr1:169256800-169271600	Weak transcription	Primary B cells from cord blood	blood
10	chr1:169256800-169278600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:169257600-169268600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:169257600-169284800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:169257800-169281200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr1:169258600-169271200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:169258600-169276400	Weak transcription	HSMM	muscle
16	chr1:169258800-169274600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:169258800-169277400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:169259200-169278600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:169259400-169274800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:169259400-169278600	Weak transcription	Adipose Nuclei	Adipose
21	chr1:169259600-169278600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:169259600-169294400	Weak transcription	Pancreas	Pancrea
23	chr1:169260400-169310400	Weak transcription	Fetal Stomach	stomach
24	chr1:169260600-169278800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr1:169262400-169271400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:169262800-169274600	Weak transcription	Liver	Liver
27	chr1:169262800-169278600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr1:169263000-169278600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:169263400-169265800	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr1:169263400-169265800	Weak transcription	Gastric	stomach
31	chr1:169263600-169267600	Weak transcription	Fetal Brain Male	brain
32	chr1:169263800-169266000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:169264000-169281400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr1:169264200-169269800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:169264200-169278600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr1:169264400-169271600	Weak transcription	Psoas Muscle	Psoas
37	chr1:169264400-169294400	Weak transcription	Left Ventricle	heart
38	chr1:169265000-169266600	Weak transcription	Primary T cells from cord blood	blood
39	chr1:169265000-169266600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr1:169265000-169278600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr1:169265000-169320400	Weak transcription	Aorta	Aorta
42	chr1:169265200-169272800	Weak transcription	HepG2	liver
43	chr1:169265200-169277200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:169265200-169278400	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr1:169265200-169281200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:169265400-169281200	Weak transcription	NHDF-Ad	bronchial
47	chr1:169265600-169266800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:169265600-169267800	Weak transcription	Primary hematopoietic stem cells	blood

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