Variant report

Variant	rs1196819
Chromosome Location	chr12:105524779-105524780
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105523431..105527512-chr12:105529193..105532336,3	MCF-7	breast:

Extended variants
information (count: 134 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10746010	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778367	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778368	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778369	0.86[EUR][1000 genomes]
rs10861347	1.00[CHB][hapmap]
rs10861371	1.00[CHB][hapmap]
rs1107755	0.83[EUR][1000 genomes]
rs1107757	0.83[EUR][1000 genomes]
rs11112424	0.83[EUR][1000 genomes]
rs11112434	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs1196742	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196745	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196756	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196759	1.00[ASN][1000 genomes]
rs1196760	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1196764	0.99[EUR][1000 genomes]
rs1196765	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196770	0.92[EUR][1000 genomes]
rs1196772	0.92[EUR][1000 genomes]
rs1196777	1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs1196780	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs1196782	0.83[EUR][1000 genomes]
rs1196786	0.83[EUR][1000 genomes]
rs1196787	0.82[EUR][1000 genomes]
rs1196789	0.82[EUR][1000 genomes]
rs1196793	1.00[CHB][hapmap];0.86[MEX][hapmap];0.83[EUR][1000 genomes]
rs1196795	0.85[CEU][hapmap];0.86[MEX][hapmap];0.81[EUR][1000 genomes]
rs1196797	0.85[CEU][hapmap];0.86[MEX][hapmap];0.83[EUR][1000 genomes]
rs1196798	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196805	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196807	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196808	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196811	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196818	1.00[CHB][hapmap]
rs1196820	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196823	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196825	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196831	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196833	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196834	0.83[EUR][1000 genomes]
rs1196839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196841	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196844	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196847	0.85[EUR][1000 genomes]
rs1196848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.83[MKK][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196851	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196852	1.00[CHB][hapmap]
rs1196853	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196857	1.00[ASN][1000 genomes]
rs1196859	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196869	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196871	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196872	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196873	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196874	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196881	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196884	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196885	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1206559	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209308	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209637	0.85[CEU][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes]
rs1211276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211277	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211626	0.83[EUR][1000 genomes]
rs12369709	0.82[EUR][1000 genomes]
rs12814458	0.83[EUR][1000 genomes]
rs12816560	0.84[EUR][1000 genomes]
rs12822081	1.00[CHB][hapmap]
rs1345096	0.89[EUR][1000 genomes]
rs1444610	0.82[EUR][1000 genomes]
rs1621553	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1663564	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1663565	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1732370	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166142	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246243	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2257156	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2374449	1.00[CEU][hapmap];0.85[GIH][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs2440692	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2440714	0.95[EUR][1000 genomes]
rs2440715	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2440718	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464173	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464175	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2464181	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464182	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35679386	0.84[EUR][1000 genomes]
rs4356312	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4356313	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4372534	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4390426	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4545651	1.00[CHB][hapmap]
rs4964122	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964331	1.00[CEU][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs6539183	1.00[CEU][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs6539186	0.85[EUR][1000 genomes]
rs6539187	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539188	0.88[EUR][1000 genomes]
rs7132040	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132624	0.90[EUR][1000 genomes]
rs7132855	1.00[CEU][hapmap];0.85[GIH][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71441895	0.92[EUR][1000 genomes]
rs7299225	1.00[CHB][hapmap]
rs7299701	0.87[EUR][1000 genomes]
rs7302854	0.85[EUR][1000 genomes]
rs7303961	0.92[EUR][1000 genomes]
rs73181823	0.84[EUR][1000 genomes]
rs7959385	1.00[CHB][hapmap]
rs7963877	1.00[CEU][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs873119	0.84[EUR][1000 genomes]
rs935240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935242	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935244	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes]
rs935246	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935248	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs935249	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	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
3	esv1826054	chr12:105505809-105568176	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1049296	chr12:105518764-105566079	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1196819	ALDH1L2	Cis_1M	lymphoblastoid	RTeQTL
rs1196819	LOC387882	cis	multi-tissue	Pritchard
rs1196819	APPL2	cis	cerebellum	SCAN
rs1196819	ALDH1L2	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105503800-105525200	Weak transcription	Fetal Heart	heart
2	chr12:105503800-105544200	Weak transcription	Aorta	Aorta
3	chr12:105505200-105530000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:105505200-105531000	Strong transcription	HMEC	breast
5	chr12:105505200-105542600	Strong transcription	Fetal Thymus	thymus
6	chr12:105505200-105559800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:105505200-105564000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr12:105505200-105567400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:105505200-105573000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:105505600-105530800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:105505600-105535200	Strong transcription	Muscle Satellite Cultured Cells	--
12	chr12:105505600-105537200	Strong transcription	Osteobl	bone
13	chr12:105505600-105550000	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr12:105505600-105573200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:105505800-105571400	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr12:105506000-105529000	Strong transcription	Primary hematopoietic stem cells	blood
17	chr12:105506000-105536800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:105506000-105537200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr12:105506400-105544600	Strong transcription	NHDF-Ad	bronchial
20	chr12:105506400-105573000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:105506600-105549200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr12:105506800-105568800	Strong transcription	Dnd41	blood
23	chr12:105506800-105572400	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr12:105507000-105528400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:105507000-105573200	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr12:105507200-105571400	Strong transcription	Primary B cells from peripheral blood	blood
27	chr12:105507400-105565600	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr12:105507600-105527800	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr12:105507600-105571400	Strong transcription	HUVEC	blood vessel
30	chr12:105507600-105572800	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr12:105507800-105563800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr12:105507800-105573200	Strong transcription	Placenta	Placenta
33	chr12:105508000-105526000	Strong transcription	GM12878-XiMat	blood
34	chr12:105508000-105549200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr12:105508000-105550400	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr12:105508000-105565400	Strong transcription	Adipose Nuclei	Adipose
37	chr12:105508200-105572800	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr12:105508400-105528000	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr12:105508400-105531800	Strong transcription	Fetal Lung	lung
40	chr12:105508400-105562000	Strong transcription	Primary B cells from cord blood	blood
41	chr12:105508600-105525800	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr12:105508600-105526400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:105508600-105532400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:105508600-105536600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr12:105508600-105573000	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr12:105508800-105565000	Strong transcription	Liver	Liver
47	chr12:105509200-105531400	Strong transcription	Duodenum Mucosa	Duodenum
48	chr12:105509400-105527200	Strong transcription	Fetal Muscle Trunk	muscle
49	chr12:105509600-105531200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:105510000-105565200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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