Variant report

Variant	rs7308474
Chromosome Location	chr12:50509583-50509584
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:50504100..50507417-chr12:50508424..50511962,5	MCF-7	breast:
2	chr12:50504789..50507930-chr12:50509010..50512332,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272368	Chromatin interaction
ENSG00000178449	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10735824	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10783338	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10876000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169278	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169281	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169282	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12369049	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369104	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12819883	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1554844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554845	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17124432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17124514	1.00[JPT][hapmap]
rs2204683	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3184122	0.86[CEU][hapmap]
rs34167640	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59262224	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6580728	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66782120	0.85[ASN][1000 genomes]
rs7135322	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7138420	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs7138945	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7294618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307469	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315690	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs7398567	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7961065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964698	0.89[EUR][1000 genomes]
rs7967979	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968119	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7972465	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7978904	0.83[EUR][1000 genomes]
rs9364	0.82[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv558840	chr12:50449976-50523964	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7308474	KIAA1463	cis	multi-tissue	Pritchard
rs7308474	CERS5	cis	Nerve Tibial	GTEx
rs7308474	DIP2B	Cis_1M	lymphoblastoid	RTeQTL
rs7308474	CERS5	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50506800-50521000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:50506800-50523600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:50507000-50510000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:50507000-50510200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr12:50507000-50510400	Weak transcription	HSMMtube	muscle
6	chr12:50507000-50513000	Weak transcription	Esophagus	oesophagus
7	chr12:50507000-50513200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:50507000-50513200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:50507000-50513600	Weak transcription	Fetal Kidney	kidney
10	chr12:50507000-50513800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:50507000-50520800	Weak transcription	Fetal Lung	lung
12	chr12:50507000-50520800	Weak transcription	NH-A	brain
13	chr12:50507000-50522400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr12:50507000-50522800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr12:50507000-50522800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr12:50507000-50523600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr12:50507000-50537400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr12:50507000-50539600	Weak transcription	Stomach Mucosa	stomach
19	chr12:50507200-50509600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:50507200-50510000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr12:50507200-50510200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:50507200-50510200	Weak transcription	NHEK	skin
23	chr12:50507200-50510400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:50507200-50512600	Weak transcription	HMEC	breast
25	chr12:50507200-50512800	Weak transcription	Brain Germinal Matrix	brain
26	chr12:50507200-50513000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr12:50507200-50513000	Weak transcription	Osteobl	bone
28	chr12:50507200-50513200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr12:50507200-50513200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:50507200-50513800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr12:50507200-50515400	Weak transcription	Fetal Brain Male	brain
32	chr12:50507200-50519000	Weak transcription	HUVEC	blood vessel
33	chr12:50507200-50520800	Weak transcription	NHDF-Ad	bronchial
34	chr12:50507200-50520800	Weak transcription	NHLF	lung
35	chr12:50507200-50521400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr12:50507200-50522600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr12:50507200-50523600	Weak transcription	Right Atrium	heart
38	chr12:50507200-50532000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr12:50507400-50513200	Weak transcription	Brain Anterior Caudate	brain
40	chr12:50507400-50514600	Genic enhancers	Primary T cells fromperipheralblood	blood
41	chr12:50508000-50509600	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr12:50508000-50509800	Weak transcription	Brain Substantia Nigra	brain
43	chr12:50508000-50510000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:50508000-50510200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr12:50508000-50510400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr12:50508000-50510400	Weak transcription	Primary B cells from cord blood	blood
47	chr12:50508000-50511200	Weak transcription	Small Intestine	intestine
48	chr12:50508000-50512800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr12:50508000-50513200	Weak transcription	Primary hematopoietic stem cells	blood
50	chr12:50508000-50513200	Weak transcription	Muscle Satellite Cultured Cells	--

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