Variant report

Variant	rs7963877
Chromosome Location	chr12:105459541-105459542
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	chr12:105446388..105448614-chr12:105457572..105460217,2	MCF-7	breast:

Extended variants
information (count: 109 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10746010	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10778367	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10778368	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10778369	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11112434	0.85[CEU][hapmap]
rs1196742	0.83[EUR][1000 genomes]
rs1196745	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1196748	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1196749	1.00[CEU][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs1196753	1.00[CEU][hapmap];0.84[TSI][hapmap]
rs1196754	1.00[CEU][hapmap]
rs1196756	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1196764	0.83[EUR][1000 genomes]
rs1196765	0.82[EUR][1000 genomes]
rs1196780	0.85[CEU][hapmap]
rs1196795	0.85[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap]
rs1196797	0.85[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap]
rs1196798	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[EUR][1000 genomes]
rs1196800	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1196801	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1196805	0.84[EUR][1000 genomes]
rs1196806	1.00[CEU][hapmap];0.85[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs1196807	0.84[EUR][1000 genomes]
rs1196808	0.83[EUR][1000 genomes]
rs1196811	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[EUR][1000 genomes]
rs1196813	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1196817	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1196819	1.00[CEU][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs1196820	0.84[EUR][1000 genomes]
rs1196823	0.83[EUR][1000 genomes]
rs1196825	0.84[EUR][1000 genomes]
rs1196831	0.84[EUR][1000 genomes]
rs1196833	0.84[EUR][1000 genomes]
rs1196839	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1196841	0.84[EUR][1000 genomes]
rs1196842	1.00[CEU][hapmap];0.82[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs1196844	0.84[EUR][1000 genomes]
rs1196848	1.00[CEU][hapmap];0.88[MKK][hapmap];0.84[EUR][1000 genomes]
rs1196851	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1196853	0.83[EUR][1000 genomes]
rs1196859	0.86[EUR][1000 genomes]
rs1196861	1.00[CEU][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs1196862	1.00[CEU][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs1196864	1.00[CEU][hapmap];0.85[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs1196869	1.00[CEU][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs1196871	0.82[EUR][1000 genomes]
rs1196872	0.92[CEU][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs1196873	1.00[CEU][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs1196874	0.84[EUR][1000 genomes]
rs1196881	0.92[CEU][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1196884	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1196885	0.87[AMR][1000 genomes]
rs1206559	0.84[EUR][1000 genomes]
rs1209308	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1209637	0.85[CEU][hapmap]
rs1211276	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1211277	0.84[EUR][1000 genomes]
rs1345096	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1621553	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1663565	0.83[EUR][1000 genomes]
rs17036705	1.00[CHD][hapmap]
rs1732370	0.84[EUR][1000 genomes]
rs2166142	0.86[EUR][1000 genomes]
rs2257156	1.00[CEU][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs2272491	1.00[CHD][hapmap]
rs2289773	1.00[CHD][hapmap]
rs2293642	1.00[CHD][hapmap]
rs2374449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2440692	0.82[EUR][1000 genomes]
rs2440714	0.85[EUR][1000 genomes]
rs2440715	1.00[ASW][hapmap];0.83[CEU][hapmap];0.82[MEX][hapmap]
rs2440718	0.84[EUR][1000 genomes]
rs2464173	0.84[EUR][1000 genomes]
rs2464175	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2464181	0.84[EUR][1000 genomes]
rs2464182	0.82[EUR][1000 genomes]
rs3794235	0.86[JPT][hapmap]
rs4356312	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4356313	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4372534	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4390426	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4964122	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4964331	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6539183	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539186	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539187	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6539188	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6539190	0.93[ASN][1000 genomes]
rs6539193	0.93[ASN][1000 genomes]
rs7132040	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7132624	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7132855	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7299166	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7299701	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7302854	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303961	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7313896	0.88[JPT][hapmap]
rs73395721	0.89[ASN][1000 genomes]
rs7973422	0.96[ASN][1000 genomes]
rs935240	1.00[CEU][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs935241	1.00[CEU][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs935242	0.84[EUR][1000 genomes]
rs935244	0.85[CEU][hapmap]
rs935246	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs935248	0.83[EUR][1000 genomes]
rs935249	0.83[EUR][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	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	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
3	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7963877	APPL2	cis	cerebellum	SCAN
rs7963877	ALDH1L2	Cis_1M	lymphoblastoid	RTeQTL
rs7963877	ALDH1L2	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105409400-105465200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr12:105413000-105476800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:105420000-105477000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr12:105431400-105461600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr12:105435600-105467400	Weak transcription	Brain Substantia Nigra	brain
6	chr12:105441200-105477000	Weak transcription	Gastric	stomach
7	chr12:105442400-105469800	Weak transcription	Fetal Lung	lung
8	chr12:105443400-105465000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:105445800-105472800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:105447000-105461600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:105447000-105464600	Weak transcription	Left Ventricle	heart
12	chr12:105447000-105468000	Weak transcription	K562	blood
13	chr12:105447000-105468600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr12:105447200-105462000	Weak transcription	Colon Smooth Muscle	Colon
15	chr12:105447200-105466800	Weak transcription	Brain Angular Gyrus	brain
16	chr12:105447200-105477200	Weak transcription	Brain Hippocampus Middle	brain
17	chr12:105448200-105461400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:105448800-105459800	Weak transcription	Ovary	ovary
19	chr12:105448800-105461200	Strong transcription	Osteobl	bone
20	chr12:105449400-105476800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr12:105450600-105461400	Strong transcription	HSMMtube	muscle
22	chr12:105450600-105461800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:105450800-105461400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:105450800-105468200	Weak transcription	Brain Anterior Caudate	brain
25	chr12:105451600-105461400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:105452000-105461200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:105452000-105464200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:105452000-105466200	Weak transcription	GM12878-XiMat	blood
29	chr12:105452200-105462000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:105453400-105460400	Strong transcription	Fetal Brain Female	brain
31	chr12:105453400-105476800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr12:105454200-105476600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr12:105455000-105461400	Weak transcription	Spleen	Spleen
34	chr12:105455600-105465200	Strong transcription	HMEC	breast
35	chr12:105455600-105467800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:105455600-105476400	Weak transcription	Fetal Brain Male	brain
37	chr12:105456000-105477000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr12:105456400-105475000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr12:105456600-105463800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr12:105456600-105475200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:105456800-105467400	Weak transcription	Fetal Stomach	stomach
42	chr12:105456800-105471200	Weak transcription	Pancreas	Pancrea
43	chr12:105456800-105476800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr12:105457800-105460400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:105457800-105462200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr12:105458000-105460800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:105458000-105461200	Strong transcription	NH-A	brain
48	chr12:105458000-105464600	Strong transcription	NHLF	lung
49	chr12:105458200-105460400	Strong transcription	Stomach Smooth Muscle	stomach
50	chr12:105458200-105460600	Strong transcription	Duodenum Smooth Muscle	Duodenum

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