Variant report

Variant	rs7957096
Chromosome Location	chr12:123544878-123544879
allele	A/G
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	chr12:123544465..123546165-chr12:123634020..123636715,2	K562	blood:
2	chr12:123544563..123545393-chr12:123557820..123558745,4	MCF-7	breast:
3	chr12:123544510..123545444-chr12:123554166..123554840,5	MCF-7	breast:
4	chr12:123544494..123545534-chr12:123553982..123555382,28	MCF-7	breast:
5	chr12:123544642..123548641-chr12:123611003..123613032,3	K562	blood:
6	chr12:123538667..123541322-chr12:123544543..123546513,3	K562	blood:
7	chr12:123544559..123546655-chr12:123548613..123551754,3	K562	blood:
8	chr12:123544494..123545483-chr12:123553982..123555382,14	MCF-7	breast:
9	chr12:123519070..123519944-chr12:123544573..123545425,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000090975	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1051434	0.96[CEU][hapmap]
rs10773921	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10846489	0.84[CEU][hapmap]
rs10848428	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11060853	0.90[JPT][hapmap]
rs11060932	0.95[YRI][hapmap]
rs11060999	0.94[YRI][hapmap]
rs11608811	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11613937	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12311043	0.94[YRI][hapmap]
rs12425009	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12425850	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1568428	0.84[CEU][hapmap]
rs1727293	0.96[CEU][hapmap];0.87[CHB][hapmap];0.80[JPT][hapmap]
rs1727295	0.91[CEU][hapmap];0.85[CHB][hapmap]
rs1727307	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1790094	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1790106	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1790121	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1790122	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1984658	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28755851	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3741530	0.96[CEU][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3759115	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3897102	0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs4148862	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4148863	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4148866	0.85[JPT][hapmap]
rs4275659	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55742290	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61955196	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61955214	0.88[ASN][1000 genomes]
rs7135296	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7296418	0.91[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7305511	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs752164	1.00[YRI][hapmap]
rs7952760	1.00[YRI][hapmap]
rs7964036	1.00[YRI][hapmap]
rs883562	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs884956	0.84[CHB][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs949143	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv832532	chr12:123395927-123573137	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv832533	chr12:123395927-123589290	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
6	nsv455732	chr12:123427573-123574838	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv560492	chr12:123427573-123574838	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv560494	chr12:123478378-123560731	Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1042550	chr12:123532028-123659500	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7957096	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs7957096	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs7957096	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs7957096	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs7957096	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs7957096	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123528600-123545800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr12:123529600-123546200	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr12:123529800-123548200	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr12:123532400-123546600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr12:123534800-123547200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:123537800-123551200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:123539400-123546600	Weak transcription	HSMMtube	muscle
8	chr12:123539600-123546000	Genic enhancers	Thymus	Thymus
9	chr12:123539600-123552600	Enhancers	Right Ventricle	heart
10	chr12:123539800-123549600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr12:123540000-123547200	Weak transcription	NH-A	brain
12	chr12:123540000-123547400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:123540600-123547400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:123541000-123545200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr12:123541000-123546600	Weak transcription	HepG2	liver
16	chr12:123541200-123545800	Weak transcription	HSMM	muscle
17	chr12:123541200-123546200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr12:123541200-123547000	Weak transcription	A549	lung
19	chr12:123541200-123548000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:123541600-123545400	Weak transcription	Pancreas	Pancrea
21	chr12:123541600-123546600	Weak transcription	Hela-S3	cervix
22	chr12:123541800-123551200	Enhancers	Fetal Muscle Leg	muscle
23	chr12:123542200-123547000	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr12:123542200-123547400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:123542200-123551200	Enhancers	Fetal Muscle Trunk	muscle
26	chr12:123542600-123546800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr12:123542600-123550400	Enhancers	NHDF-Ad	bronchial
28	chr12:123542600-123550600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:123542600-123550800	Enhancers	Placenta	Placenta
30	chr12:123542800-123545200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:123542800-123546000	Enhancers	Brain Angular Gyrus	brain
32	chr12:123542800-123547000	Enhancers	Fetal Heart	heart
33	chr12:123542800-123563800	Enhancers	Left Ventricle	heart
34	chr12:123543000-123546600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr12:123543000-123547600	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr12:123543000-123549600	Enhancers	NHLF	lung
37	chr12:123543000-123551400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:123543200-123545200	Enhancers	Colon Smooth Muscle	Colon
39	chr12:123543200-123545200	Enhancers	Fetal Stomach	stomach
40	chr12:123543200-123546200	Weak transcription	Primary B cells from peripheral blood	blood
41	chr12:123543200-123547000	Enhancers	Ovary	ovary
42	chr12:123543200-123548800	Enhancers	Brain Anterior Caudate	brain
43	chr12:123543200-123549000	Enhancers	Adipose Nuclei	Adipose
44	chr12:123543200-123552600	Enhancers	Lung	lung
45	chr12:123543400-123545600	Enhancers	Brain Cingulate Gyrus	brain
46	chr12:123543400-123545600	Enhancers	Brain Substantia Nigra	brain
47	chr12:123543400-123546400	Weak transcription	Primary B cells from cord blood	blood
48	chr12:123543400-123548800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr12:123543400-123550200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:123543400-123551000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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