Variant report

Variant	rs1196865
Chromosome Location	chr12:105569486-105569487
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10861327	0.80[GIH][hapmap];0.83[MEX][hapmap]
rs10861328	0.80[GIH][hapmap];0.83[MEX][hapmap]
rs11112347	0.80[GIH][hapmap];0.83[MEX][hapmap]
rs11112414	0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11610656	0.82[ASN][1000 genomes]
rs1196750	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1196752	0.82[AFR][1000 genomes]
rs1196758	0.81[YRI][hapmap]
rs1196761	0.96[CEU][hapmap];0.83[TSI][hapmap]
rs1196766	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.85[ASN][1000 genomes]
rs1196767	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.85[ASN][1000 genomes]
rs1196768	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs1196781	0.90[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap]
rs1196788	0.90[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap]
rs1196796	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs1196803	0.97[ASN][1000 genomes]
rs1196804	0.91[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1196809	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1196810	0.96[ASN][1000 genomes]
rs1196812	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1196814	0.92[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1196816	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1196821	0.92[ASN][1000 genomes]
rs1196822	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1196826	0.94[ASN][1000 genomes]
rs1196827	0.94[ASN][1000 genomes]
rs1196828	0.94[ASN][1000 genomes]
rs1196829	0.94[ASN][1000 genomes]
rs1196835	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1196836	0.92[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap];0.87[YRI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1196837	0.93[ASN][1000 genomes]
rs1196838	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[ASN][1000 genomes]
rs1196840	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1196843	0.90[ASN][1000 genomes]
rs1196846	0.94[ASN][1000 genomes]
rs1196850	0.92[ASN][1000 genomes]
rs1196854	0.93[AFR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1196855	0.94[ASN][1000 genomes]
rs1196856	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1196858	0.96[ASN][1000 genomes]
rs1196860	0.93[AFR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1196866	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196867	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196868	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196870	0.97[ASN][1000 genomes]
rs1196876	0.97[ASN][1000 genomes]
rs1196877	0.97[ASN][1000 genomes]
rs1196878	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1196883	0.84[CHD][hapmap]
rs1201657	0.92[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1201658	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12581638	0.82[GIH][hapmap];0.83[MEX][hapmap]
rs17036869	0.85[CHB][hapmap]
rs1732371	0.91[ASN][1000 genomes]
rs1732378	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1732379	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1732384	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2246510	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs2264066	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2374448	0.90[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap]
rs2440708	0.85[JPT][hapmap]
rs2440713	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2440717	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2440719	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs727888	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs7308195	0.82[GIH][hapmap];0.83[MEX][hapmap]
rs7310488	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs752471	0.96[CEU][hapmap];0.83[TSI][hapmap]
rs7954946	0.81[CEU][hapmap]
rs9143	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv870352	chr12:105557770-105589263	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1196865	ALDH1L2	cis	cerebellum	SCAN
rs1196865	C12orf45	cis	cerebellum	SCAN
rs1196865	APPL2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105505200-105573000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr12:105505600-105573200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:105505800-105571400	Strong transcription	Rectal Mucosa Donor 31	rectum
4	chr12:105506400-105573000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:105506800-105572400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr12:105507000-105573200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr12:105507200-105571400	Strong transcription	Primary B cells from peripheral blood	blood
8	chr12:105507600-105571400	Strong transcription	HUVEC	blood vessel
9	chr12:105507600-105572800	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr12:105507800-105573200	Strong transcription	Placenta	Placenta
11	chr12:105508200-105572800	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr12:105508600-105573000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr12:105518600-105573200	Strong transcription	HSMM	muscle
14	chr12:105522600-105586000	Weak transcription	Stomach Mucosa	stomach
15	chr12:105524600-105578200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:105525400-105583200	Weak transcription	Fetal Heart	heart
17	chr12:105529800-105571400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:105532400-105577800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:105546800-105625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr12:105555200-105573200	Strong transcription	A549	lung
21	chr12:105556200-105583400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr12:105557400-105571600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:105557600-105578000	Weak transcription	Gastric	stomach
24	chr12:105558200-105578200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:105558200-105578400	Weak transcription	Right Ventricle	heart
26	chr12:105558200-105587200	Weak transcription	Psoas Muscle	Psoas
27	chr12:105558400-105578000	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr12:105558800-105615200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr12:105559400-105578800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:105560800-105581800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr12:105561000-105572600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:105561400-105598400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr12:105561600-105572800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:105561600-105572800	Strong transcription	NHDF-Ad	bronchial
35	chr12:105561600-105573600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:105561800-105573200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:105562400-105571600	Strong transcription	Fetal Intestine Large	intestine
38	chr12:105563000-105571400	Strong transcription	Fetal Thymus	thymus
39	chr12:105563000-105573400	Strong transcription	Primary B cells from cord blood	blood
40	chr12:105563200-105572000	Strong transcription	Primary T cells from cord blood	blood
41	chr12:105563200-105573200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr12:105563400-105571400	Strong transcription	Duodenum Mucosa	Duodenum
43	chr12:105563800-105570400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr12:105564000-105582200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr12:105564600-105571200	Strong transcription	Placenta Amnion	Placenta Amnion
46	chr12:105564800-105571400	Strong transcription	HMEC	breast
47	chr12:105565000-105577800	Weak transcription	Colon Smooth Muscle	Colon
48	chr12:105565200-105569600	Strong transcription	Fetal Muscle Trunk	muscle
49	chr12:105565400-105572000	Strong transcription	Left Ventricle	heart
50	chr12:105566000-105571000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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