Variant report

Variant	rs11112347
Chromosome Location	chr12:105446831-105446832
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:105073708..105074536-chr12:105446439..105447355,3	MCF-7	breast:
2	chr12:104595044..104595663-chr12:105446789..105447301,2	MCF-7	breast:
3	chr12:104741125..104741819-chr12:105446589..105447468,2	MCF-7	breast:
4	chr12:105312658..105314967-chr12:105446704..105448489,2	K562	blood:
5	chr12:104594663..104595632-chr12:105446526..105447442,3	K562	blood:
6	chr12:104775747..104776264-chr12:105446543..105447108,2	K562	blood:
7	chr12:105435675..105437958-chr12:105444796..105446919,2	K562	blood:
8	chr12:105446119..105448037-chr12:105501270..105503403,2	MCF-7	breast:
9	chr12:105446388..105448614-chr12:105457572..105460217,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000136051	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10778366	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10861327	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861328	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10861329	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10861330	1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10861331	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10861332	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10861333	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10861335	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10861336	1.00[CEU][hapmap];0.80[CHB][hapmap];0.81[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11112349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112350	1.00[CEU][hapmap];0.80[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11112351	1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11112352	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11112356	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11112414	0.81[CHD][hapmap]
rs11611105	0.91[CHD][hapmap]
rs11611857	0.84[ASN][1000 genomes]
rs11612252	1.00[CEU][hapmap];0.82[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11613233	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11613261	1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1196758	0.81[CEU][hapmap]
rs1196766	0.85[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap]
rs1196767	0.85[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap]
rs1196768	0.91[CEU][hapmap]
rs1196781	0.85[CEU][hapmap];0.96[MEX][hapmap]
rs1196788	0.85[CEU][hapmap];0.92[MEX][hapmap]
rs1196796	0.85[CEU][hapmap]
rs1196804	0.85[CEU][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap]
rs1196814	0.85[CEU][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap]
rs1196836	0.85[CEU][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap]
rs1196838	0.82[CEU][hapmap]
rs1196865	0.80[GIH][hapmap];0.83[MEX][hapmap]
rs1196878	0.81[CEU][hapmap]
rs1196879	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1196880	0.83[ASN][1000 genomes]
rs1196882	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1196883	0.95[CHD][hapmap];0.82[ASN][1000 genomes]
rs1196886	0.82[ASN][1000 genomes]
rs1201657	0.85[CEU][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap]
rs12367626	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12581638	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17242777	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1732377	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1732378	0.81[CEU][hapmap]
rs2246510	0.85[CEU][hapmap]
rs2264066	0.85[CEU][hapmap]
rs2374448	0.85[CEU][hapmap];0.92[MEX][hapmap]
rs2374451	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2440693	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2440708	0.84[CEU][hapmap]
rs2440713	0.81[CHD][hapmap]
rs2440717	0.84[CEU][hapmap]
rs4144467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4144468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56118650	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56188643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56369757	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61938827	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs727888	0.85[CEU][hapmap]
rs7308195	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7310488	0.85[CEU][hapmap]
rs7311691	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73179949	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7962686	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9143	0.81[CHD][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11112347	APPL2	cis	cerebellum	SCAN
rs11112347	ALDH1L2	cis	cerebellum	SCAN

Chromatin state (count:72 , 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	chr12:105413200-105457800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr12:105414800-105447200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:105414800-105454000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr12:105420000-105477000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr12:105420400-105448600	Weak transcription	Ovary	ovary
8	chr12:105420600-105447000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:105423200-105459400	Weak transcription	Lung	lung
10	chr12:105431400-105461600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr12:105431800-105454800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:105432200-105454600	Weak transcription	NHEK	skin
13	chr12:105434000-105453000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr12:105435200-105453600	Weak transcription	Fetal Stomach	stomach
15	chr12:105435600-105467400	Weak transcription	Brain Substantia Nigra	brain
16	chr12:105437200-105448600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr12:105440200-105449800	Strong transcription	HSMMtube	muscle
18	chr12:105440400-105448600	Strong transcription	HSMM	muscle
19	chr12:105441200-105477000	Weak transcription	Gastric	stomach
20	chr12:105441400-105453400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:105441400-105454800	Weak transcription	Pancreas	Pancrea
22	chr12:105441600-105448800	Weak transcription	A549	lung
23	chr12:105441600-105458200	Weak transcription	Right Ventricle	heart
24	chr12:105442400-105448400	Weak transcription	Aorta	Aorta
25	chr12:105442400-105448800	Weak transcription	Fetal Muscle Leg	muscle
26	chr12:105442400-105451000	Weak transcription	Fetal Brain Male	brain
27	chr12:105442400-105469800	Weak transcription	Fetal Lung	lung
28	chr12:105443400-105465000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr12:105443600-105448800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:105443800-105448200	Weak transcription	Brain Germinal Matrix	brain
31	chr12:105443800-105453000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr12:105444000-105453600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr12:105444200-105449200	Weak transcription	Fetal Brain Female	brain
34	chr12:105444400-105447000	Weak transcription	Adipose Nuclei	Adipose
35	chr12:105445200-105447200	Enhancers	Primary B cells from peripheral blood	blood
36	chr12:105445200-105453200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr12:105445400-105447200	Enhancers	GM12878-XiMat	blood
38	chr12:105445400-105448400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr12:105445400-105448800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr12:105445400-105453200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr12:105445800-105448200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:105445800-105448400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:105445800-105472800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr12:105446000-105448200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:105446200-105448800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:105446400-105447000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr12:105446400-105447000	Strong transcription	K562	blood
48	chr12:105446400-105448000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:105446600-105447000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:105446600-105447000	Enhancers	Duodenum Smooth Muscle	Duodenum

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