Variant report

Variant	rs10861359
Chromosome Location	chr12:105561991-105561992
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105557729..105562363-chr12:105563109..105566794,6	K562	blood:
2	chr12:105559645..105562741-chr12:105564536..105567836,4	K562	blood:
3	chr12:105561858..105564430-chr12:105566394..105568503,2	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1014502	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10431460	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10459203	0.82[CEU][hapmap];0.81[CHD][hapmap]
rs10459204	0.82[CEU][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap]
rs1057110	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1077896	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10861334	0.80[CEU][hapmap]
rs10861339	0.81[CEU][hapmap]
rs10861361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10861363	0.84[CEU][hapmap]
rs1109433	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11112369	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11112370	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11112372	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11112375	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11112376	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11112379	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11112388	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112409	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112412	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11112415	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11112416	1.00[CEU][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11112421	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11112423	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11112432	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11831854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11832489	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11834277	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12228093	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12228948	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12230762	0.82[ASN][1000 genomes]
rs12812433	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12815031	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12819309	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12823614	0.82[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap]
rs12830078	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1317955	1.00[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs1373552	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1444611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1470381	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2166143	0.87[CEU][hapmap];0.80[CHD][hapmap];0.86[MEX][hapmap]
rs2272495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2293643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2293644	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2464176	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28549976	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34075890	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34119882	0.80[ASN][1000 genomes]
rs34983773	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35462155	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35672903	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3736628	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3794222	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3794223	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3794224	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3794227	0.94[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3817607	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3829296	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4964125	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4964334	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4964335	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4964336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4964338	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964339	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4964340	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4964342	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55908437	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56693261	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73179994	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7485364	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs755604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8015	0.92[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs881279	1.00[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9919746	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][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	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	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
3	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
4	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10861359	APPL2	cis	cerebellum	SCAN
rs10861359	KIAA1033	cis	cerebellum	SCAN
rs10861359	C12orf75	cis	cerebellum	SCAN
rs10861359	TDG	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105505200-105564000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr12:105505200-105567400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:105505200-105573000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:105505600-105573200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:105505800-105571400	Strong transcription	Rectal Mucosa Donor 31	rectum
6	chr12:105506400-105573000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:105506800-105568800	Strong transcription	Dnd41	blood
8	chr12:105506800-105572400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr12:105507000-105573200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr12:105507200-105571400	Strong transcription	Primary B cells from peripheral blood	blood
11	chr12:105507400-105565600	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr12:105507600-105571400	Strong transcription	HUVEC	blood vessel
13	chr12:105507600-105572800	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr12:105507800-105563800	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr12:105507800-105573200	Strong transcription	Placenta	Placenta
16	chr12:105508000-105565400	Strong transcription	Adipose Nuclei	Adipose
17	chr12:105508200-105572800	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr12:105508400-105562000	Strong transcription	Primary B cells from cord blood	blood
19	chr12:105508600-105573000	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:105508800-105565000	Strong transcription	Liver	Liver
21	chr12:105510000-105565200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:105513800-105567800	Weak transcription	Pancreas	Pancrea
23	chr12:105518600-105573200	Strong transcription	HSMM	muscle
24	chr12:105522600-105586000	Weak transcription	Stomach Mucosa	stomach
25	chr12:105524600-105578200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:105525400-105583200	Weak transcription	Fetal Heart	heart
27	chr12:105527200-105565400	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr12:105529800-105571400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:105532400-105577800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:105533200-105565200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:105539800-105565800	Strong transcription	Osteobl	bone
32	chr12:105546800-105625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr12:105549200-105567400	Weak transcription	Fetal Brain Male	brain
34	chr12:105549200-105567800	Weak transcription	Esophagus	oesophagus
35	chr12:105549800-105567200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:105549800-105567200	Weak transcription	Brain Angular Gyrus	brain
37	chr12:105550800-105562000	Strong transcription	Duodenum Mucosa	Duodenum
38	chr12:105551000-105562400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:105551000-105565200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr12:105551000-105565600	Strong transcription	NH-A	brain
41	chr12:105551200-105562000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr12:105552000-105565200	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr12:105553400-105564600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr12:105554600-105564000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr12:105555000-105562000	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr12:105555200-105573200	Strong transcription	A549	lung
47	chr12:105556200-105583400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr12:105557400-105571600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:105557600-105565000	Strong transcription	GM12878-XiMat	blood
50	chr12:105557600-105567200	Weak transcription	Fetal Intestine Small	intestine

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