Variant report

Variant	rs11112416
Chromosome Location	chr12:105618561-105618562
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105616267..105619374-chr12:105619746..105623496,4	MCF-7	breast:
2	chr12:105606787..105609967-chr12:105617120..105620044,3	MCF-7	breast:
3	chr12:105604459..105610765-chr12:105612400..105619000,9	MCF-7	breast:
4	chr12:105609229..105612971-chr12:105615964..105620947,4	K562	blood:
5	chr12:105606795..105619301-chr12:105624368..105633184,26	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136044	Chromatin interaction
ENSG00000235162	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1014502	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10431460	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10459203	0.82[CEU][hapmap]
rs10459204	0.82[CEU][hapmap]
rs1057110	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1077896	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10861334	0.80[CEU][hapmap]
rs10861339	0.81[CEU][hapmap]
rs10861359	1.00[CEU][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10861361	1.00[CEU][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10861363	0.84[CEU][hapmap]
rs1107756	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1109433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112369	0.87[EUR][1000 genomes]
rs11112370	1.00[CEU][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs11112372	0.83[EUR][1000 genomes]
rs11112375	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11112376	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11112379	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11112388	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11112409	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11112412	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11112415	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11112421	1.00[CEU][hapmap];0.80[GIH][hapmap];0.86[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11112423	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11112432	1.00[CEU][hapmap];0.80[GIH][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11831854	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11832489	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11834277	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1196751	0.90[CHB][hapmap]
rs1196758	0.90[CHB][hapmap]
rs1196769	0.80[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs1196771	0.98[ASN][1000 genomes]
rs1196773	0.98[ASN][1000 genomes]
rs1196794	0.98[ASN][1000 genomes]
rs1196845	0.90[CHB][hapmap]
rs12228093	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12228948	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12812433	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12815031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12819309	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12823614	0.82[CEU][hapmap]
rs1317955	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1373552	1.00[CEU][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1444611	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1470381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2166143	0.87[CEU][hapmap]
rs2246510	0.90[CHB][hapmap]
rs2272495	1.00[CEU][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2293643	1.00[CEU][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2293644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2440695	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2440706	0.98[ASN][1000 genomes]
rs2464184	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[ASN][1000 genomes]
rs28549976	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34075890	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34983773	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35462155	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35672903	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3736628	0.84[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3794222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3794223	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3794224	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3794227	1.00[ASW][hapmap];0.94[CEU][hapmap];0.87[GIH][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3817607	1.00[CEU][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3829296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4964125	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4964334	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4964335	0.87[EUR][1000 genomes]
rs4964336	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4964338	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4964339	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4964340	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4964342	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56693261	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73179994	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7485364	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs755604	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8015	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs880797	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs881279	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9919746	0.88[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	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	nsv455704	chr12:105583877-105651356	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
3	nsv560053	chr12:105583877-105651356	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
4	nsv899499	chr12:105616297-105722529	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11112416	KIAA1033	cis	cerebellum	SCAN
rs11112416	APPL2	cis	cerebellum	SCAN
rs11112416	C12orf75	cis	cerebellum	SCAN
rs11112416	TDG	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105546800-105625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:105578000-105623200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr12:105578200-105620000	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr12:105584000-105627000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:105590200-105620000	Strong transcription	Primary T helper cells PMA-I stimulated	--
6	chr12:105590400-105618800	Strong transcription	Primary B cells from peripheral blood	blood
7	chr12:105591000-105619400	Strong transcription	Primary T cells from cord blood	blood
8	chr12:105595000-105618800	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr12:105596400-105621800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:105600800-105626800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:105601000-105619200	Weak transcription	GM12878-XiMat	blood
12	chr12:105605600-105628400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:105607200-105618600	Genic enhancers	Fetal Intestine Large	intestine
14	chr12:105609000-105618600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:105609200-105620400	Genic enhancers	Fetal Intestine Small	intestine
16	chr12:105609200-105622400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:105609200-105626800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr12:105609200-105628600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr12:105609400-105618600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr12:105609400-105619400	Strong transcription	Osteobl	bone
21	chr12:105610200-105618800	Strong transcription	Thymus	Thymus
22	chr12:105610800-105620000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr12:105611000-105620000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr12:105611000-105620200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:105611200-105620200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr12:105611200-105621200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr12:105611200-105628200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr12:105611400-105619600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:105611400-105621200	Weak transcription	Hela-S3	cervix
30	chr12:105611600-105621200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr12:105611600-105621600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr12:105611600-105626200	Weak transcription	Fetal Brain Male	brain
33	chr12:105611800-105621200	Weak transcription	Fetal Kidney	kidney
34	chr12:105612000-105624800	Genic enhancers	NHDF-Ad	bronchial
35	chr12:105612200-105618600	Enhancers	Right Atrium	heart
36	chr12:105612600-105618800	Strong transcription	NHEK	skin
37	chr12:105612800-105618600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:105612800-105624200	Strong transcription	Fetal Stomach	stomach
39	chr12:105613000-105623600	Strong transcription	Fetal Muscle Trunk	muscle
40	chr12:105613200-105620000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr12:105613800-105618800	Strong transcription	HSMM	muscle
42	chr12:105613800-105622000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:105614200-105619200	Genic enhancers	Rectal Mucosa Donor 31	rectum
44	chr12:105614400-105619200	Genic enhancers	Left Ventricle	heart
45	chr12:105614800-105618600	Genic enhancers	Brain Anterior Caudate	brain
46	chr12:105615200-105618800	Genic enhancers	Duodenum Mucosa	Duodenum
47	chr12:105615400-105618600	Genic enhancers	Brain Inferior Temporal Lobe	brain
48	chr12:105615600-105618600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:105615600-105619400	Weak transcription	HUVEC	blood vessel
50	chr12:105615800-105620000	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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