Variant report

Variant	rs1896027
Chromosome Location	chr12:45697872-45697873
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1004598	0.91[AFR][1000 genomes]
rs1019584	0.80[ASW][hapmap];0.82[LWK][hapmap];0.95[MKK][hapmap];0.83[AFR][1000 genomes]
rs1025088	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10492285	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs10736024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10748416	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10748417	0.81[AFR][1000 genomes]
rs10748418	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10748420	0.80[YRI][hapmap];0.88[AFR][1000 genomes]
rs10785559	0.83[AFR][1000 genomes]
rs10785564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10785565	0.85[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10785568	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10880773	0.87[AFR][1000 genomes]
rs11182971	0.83[AMR][1000 genomes]
rs11182980	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1238407	0.83[AFR][1000 genomes]
rs12578188	1.00[CEU][hapmap]
rs12578220	1.00[CEU][hapmap]
rs12578314	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs12579080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12580320	1.00[CEU][hapmap]
rs12581525	1.00[CEU][hapmap]
rs12581554	1.00[CEU][hapmap]
rs12582025	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12582369	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap]
rs17095441	1.00[CEU][hapmap]
rs17095584	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap]
rs17095688	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17095706	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17095713	1.00[CEU][hapmap]
rs17095716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17095721	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17095722	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17095723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17095736	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs17095784	1.00[CEU][hapmap]
rs17095866	1.00[CEU][hapmap]
rs17095888	1.00[CEU][hapmap]
rs17095911	1.00[CEU][hapmap]
rs1862907	0.83[AMR][1000 genomes]
rs1877972	0.83[AMR][1000 genomes]
rs1913691	0.80[YRI][hapmap];0.88[AFR][1000 genomes]
rs2037855	0.80[YRI][hapmap];0.90[AFR][1000 genomes]
rs2037856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2037857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2077715	0.85[LWK][hapmap]
rs3920257	1.00[CEU][hapmap]
rs41331147	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap]
rs4489808	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4768087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4768600	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768604	0.83[AMR][1000 genomes]
rs4768605	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6582542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6582543	0.83[AMR][1000 genomes]
rs7135029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136281	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304389	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap]
rs7304749	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307262	0.82[ASW][hapmap]
rs7486228	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7953360	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7960422	0.88[AFR][1000 genomes]
rs7970250	1.00[ASW][hapmap];0.97[LWK][hapmap];0.97[MKK][hapmap];0.80[YRI][hapmap];0.91[AFR][1000 genomes]
rs7970619	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050923	chr12:45581310-45808289	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv690	chr12:45674127-45718859	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
3	nsv826357	chr12:45691091-45740769	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45654400-45725600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:45666200-45709200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr12:45674200-45706800	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr12:45675800-45709000	Weak transcription	Lung	lung
5	chr12:45676400-45740400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:45677600-45698200	Weak transcription	Primary T cells from cord blood	blood
7	chr12:45680000-45736800	Weak transcription	Fetal Intestine Small	intestine
8	chr12:45681000-45698200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr12:45683600-45709400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr12:45684400-45721800	Weak transcription	Esophagus	oesophagus
11	chr12:45685800-45698200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr12:45686200-45707000	Weak transcription	Primary B cells from cord blood	blood
13	chr12:45691000-45708600	Weak transcription	Stomach Mucosa	stomach
14	chr12:45691000-45708800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr12:45692400-45709000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:45692400-45721200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:45692800-45707000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr12:45693000-45707400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:45693000-45744000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr12:45693200-45703600	Weak transcription	HSMM	muscle
21	chr12:45693200-45708800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:45693200-45725400	Weak transcription	Fetal Kidney	kidney
23	chr12:45693400-45698000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:45693400-45698000	Weak transcription	Fetal Stomach	stomach
25	chr12:45693400-45702400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:45693600-45698000	Weak transcription	Placenta	Placenta
27	chr12:45693600-45698000	Weak transcription	Pancreas	Pancrea
28	chr12:45693600-45703000	Weak transcription	NHLF	lung
29	chr12:45693600-45703000	Weak transcription	Osteobl	bone
30	chr12:45693600-45707000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr12:45693600-45707600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:45693600-45709000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr12:45693600-45730600	Weak transcription	NH-A	brain
34	chr12:45693800-45721800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr12:45694200-45698600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr12:45695000-45700000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr12:45695200-45741800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr12:45695600-45701600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:45696000-45698000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:45696000-45698200	Enhancers	HUVEC	blood vessel
41	chr12:45696000-45698800	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr12:45696000-45701600	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr12:45696000-45702600	Strong transcription	Fetal Thymus	thymus
44	chr12:45696200-45699800	Enhancers	Colon Smooth Muscle	Colon
45	chr12:45696200-45708600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr12:45696400-45699200	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr12:45696400-45699400	Weak transcription	NHDF-Ad	bronchial
48	chr12:45696400-45736600	Weak transcription	HepG2	liver
49	chr12:45696600-45698000	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr12:45696600-45700000	Enhancers	Fetal Heart	heart

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