Variant report

Variant	rs7967979
Chromosome Location	chr12:50520676-50520677
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50519576..50522320-chr12:50527262..50529699,2	K562	blood:
2	chr12:50481941..50484070-chr12:50519129..50521598,2	MCF-7	breast:
3	chr12:50503355..50506144-chr12:50519639..50521330,2	K562	blood:
4	chr12:50513121..50517277-chr12:50517671..50521204,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066117	Chromatin interaction
ENSG00000139624	Chromatin interaction
ENSG00000272368	Chromatin interaction
ENSG00000178449	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10735824	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10783338	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10876000	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169278	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169281	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169282	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12369049	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369104	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12819883	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1554844	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554845	0.91[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17124432	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2204683	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3184122	0.83[CEU][hapmap]
rs34167640	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741562	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59262224	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6580728	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66782120	0.85[ASN][1000 genomes]
rs7135322	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7138945	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7294618	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307230	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307469	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308474	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7398567	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7961065	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961112	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964698	0.87[EUR][1000 genomes]
rs7968119	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7972465	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7978904	0.84[EUR][1000 genomes]
rs9364	0.80[CEU][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
rs7967979	DIP2B	Cis_1M	lymphoblastoid	RTeQTL
rs7967979	CERS5	cis	Nerve Tibial	GTEx
rs7967979	KIAA1463	cis	multi-tissue	Pritchard
rs7967979	DIP2B	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 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	chr12:50507000-50520800	Weak transcription	Fetal Lung	lung
4	chr12:50507000-50520800	Weak transcription	NH-A	brain
5	chr12:50507000-50522400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr12:50507000-50522800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr12:50507000-50522800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:50507000-50523600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:50507000-50537400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr12:50507000-50539600	Weak transcription	Stomach Mucosa	stomach
11	chr12:50507200-50520800	Weak transcription	NHDF-Ad	bronchial
12	chr12:50507200-50520800	Weak transcription	NHLF	lung
13	chr12:50507200-50521400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr12:50507200-50522600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr12:50507200-50523600	Weak transcription	Right Atrium	heart
16	chr12:50507200-50532000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr12:50509400-50521600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr12:50509400-50522600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr12:50510800-50523800	Weak transcription	Psoas Muscle	Psoas
20	chr12:50510800-50528400	Strong transcription	Liver	Liver
21	chr12:50511200-50538200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:50511400-50538600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:50512600-50522800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:50512600-50529200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:50512600-50538200	Strong transcription	Primary B cells from cord blood	blood
26	chr12:50513000-50522200	Strong transcription	Stomach Smooth Muscle	stomach
27	chr12:50513200-50521200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr12:50514200-50522800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr12:50514400-50520800	Weak transcription	Fetal Kidney	kidney
30	chr12:50514400-50520800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr12:50514800-50523600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr12:50515000-50521200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr12:50515400-50521200	Weak transcription	HSMMtube	muscle
34	chr12:50515400-50522400	Weak transcription	K562	blood
35	chr12:50515600-50523800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:50515800-50523600	Weak transcription	HepG2	liver
37	chr12:50515800-50523800	Weak transcription	Fetal Brain Male	brain
38	chr12:50516000-50532400	Strong transcription	Duodenum Mucosa	Duodenum
39	chr12:50516600-50536200	Strong transcription	Fetal Intestine Large	intestine
40	chr12:50517400-50520800	Weak transcription	NHEK	skin
41	chr12:50517600-50520800	Weak transcription	Spleen	Spleen
42	chr12:50517600-50523000	Weak transcription	Fetal Brain Female	brain
43	chr12:50517600-50548000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr12:50517800-50520800	Weak transcription	Pancreas	Pancrea
45	chr12:50518000-50520800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:50518000-50520800	Weak transcription	Ovary	ovary
47	chr12:50518000-50520800	Weak transcription	Thymus	Thymus
48	chr12:50518000-50521000	Weak transcription	Gastric	stomach
49	chr12:50518000-50521000	Weak transcription	Left Ventricle	heart
50	chr12:50518000-50521400	Weak transcription	Right Ventricle	heart

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