Variant report

Variant	rs12077442
Chromosome Location	chr1:98370375-98370376
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10747488	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs10747489	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes]
rs10747490	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10747491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10747492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875111	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875120	0.94[ASN][1000 genomes]
rs11165920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11165921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11165934	0.82[ASN][1000 genomes]
rs11165938	0.82[ASN][1000 genomes]
rs11165939	0.82[ASN][1000 genomes]
rs11165940	0.82[ASN][1000 genomes]
rs1198591	1.00[JPT][hapmap]
rs1198592	1.00[JPT][hapmap]
rs1198593	1.00[JPT][hapmap]
rs1198594	1.00[JPT][hapmap]
rs12060207	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs12062845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12067567	0.82[ASN][1000 genomes]
rs12067700	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12068763	0.82[ASN][1000 genomes]
rs12069474	0.82[ASN][1000 genomes]
rs12071067	0.82[ASN][1000 genomes]
rs12072739	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12073487	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12089031	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12406713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17379561	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1801265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2660303	1.00[JPT][hapmap]
rs2660304	1.00[JPT][hapmap]
rs4246515	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4294451	0.94[ASN][1000 genomes]
rs4322261	0.82[ASN][1000 genomes]
rs4372296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4375301	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4378243	0.88[ASN][1000 genomes]
rs4379706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4394693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4394694	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4399192	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4421623	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4423049	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4456128	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4478846	0.88[ASN][1000 genomes]
rs4495746	0.85[ASN][1000 genomes]
rs4506495	1.00[JPT][hapmap]
rs4523551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4523552	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4546957	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs45522136	0.81[ASN][1000 genomes]
rs4598523	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4970719	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4970720	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4970721	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4970722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4970723	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4970725	0.94[ASN][1000 genomes]
rs56732321	0.82[ASN][1000 genomes]
rs57468345	0.82[ASN][1000 genomes]
rs61787782	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61787783	0.87[ASN][1000 genomes]
rs61787784	0.87[ASN][1000 genomes]
rs61787785	0.87[ASN][1000 genomes]
rs61787819	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61787820	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61787823	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61787824	0.94[ASN][1000 genomes]
rs61787826	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61787827	0.94[ASN][1000 genomes]
rs61787828	0.82[ASN][1000 genomes]
rs61787829	0.88[ASN][1000 genomes]
rs61787830	0.88[ASN][1000 genomes]
rs6604093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6604098	0.88[ASN][1000 genomes]
rs6658412	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6664489	0.82[ASN][1000 genomes]
rs6677116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6692580	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6703588	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7415086	0.94[ASN][1000 genomes]
rs7418577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7524038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7526108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7552188	0.82[EUR][1000 genomes]
rs9324374	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9324378	0.82[ASN][1000 genomes]
rs9661794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9662232	0.94[ASN][1000 genomes]
rs9662719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9662870	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9727548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9727976	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9729190	0.82[ASN][1000 genomes]
rs9729897	0.94[ASN][1000 genomes]
rs9887831	0.82[ASN][1000 genomes]
rs9887848	0.82[ASN][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	nsv530049	chr1:97883261-98384614	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1012958	chr1:98081528-98864746	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv871625	chr1:98165091-98564736	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv830725	chr1:98257894-98443497	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv934244	chr1:98260729-98415915	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv871077	chr1:98274132-98541677	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:98364600-98377200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr1:98365000-98371000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr1:98366800-98370400	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr1:98367000-98371000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:98367000-98375800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr1:98367200-98370400	Weak transcription	Primary B cells from cord blood	blood
7	chr1:98367200-98373200	Enhancers	NHDF-Ad	bronchial
8	chr1:98367400-98370400	Enhancers	HUVEC	blood vessel
9	chr1:98367400-98382200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:98368000-98376800	Weak transcription	Primary T cells from cord blood	blood
11	chr1:98368000-98377000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:98368000-98384000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:98368600-98371000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr1:98368600-98376000	Weak transcription	Dnd41	blood
15	chr1:98368600-98377000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr1:98368800-98370600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:98368800-98371200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:98369000-98370400	Enhancers	Liver	Liver
19	chr1:98369000-98370800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:98369000-98371000	Enhancers	Colon Smooth Muscle	Colon
21	chr1:98369000-98371200	Enhancers	NHLF	lung
22	chr1:98369200-98370800	Enhancers	HMEC	breast
23	chr1:98369200-98372200	Enhancers	NH-A	brain
24	chr1:98369400-98370400	Enhancers	Brain Anterior Caudate	brain
25	chr1:98369400-98370400	Enhancers	Fetal Brain Male	brain
26	chr1:98369400-98370800	Enhancers	Hela-S3	cervix
27	chr1:98369400-98371200	Enhancers	Brain Substantia Nigra	brain
28	chr1:98369400-98372000	Enhancers	Brain Hippocampus Middle	brain
29	chr1:98369600-98370400	Enhancers	Fetal Lung	lung
30	chr1:98369600-98371200	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:98369600-98373600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:98369800-98371200	Enhancers	Brain Angular Gyrus	brain
33	chr1:98369800-98371600	Weak transcription	Psoas Muscle	Psoas
34	chr1:98369800-98372200	Weak transcription	HSMMtube	muscle
35	chr1:98369800-98373000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:98369800-98373600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr1:98369800-98384000	Weak transcription	Right Atrium	heart
38	chr1:98370000-98370400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:98370000-98370800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr1:98370000-98372400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:98370000-98373400	Weak transcription	Adipose Nuclei	Adipose
42	chr1:98370000-98376000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr1:98370200-98370600	Enhancers	Osteobl	bone
44	chr1:98370200-98371000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr1:98370200-98371400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:98370200-98371600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:98370200-98371600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr1:98370200-98372000	Weak transcription	HSMM	muscle
49	chr1:98370200-98372200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:98370200-98372200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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