Variant report

Variant	rs10773921
Chromosome Location	chr12:123541606-123541607
allele	C/T
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123538842..123542281-chr12:123553945..123556285,3	MCF-7	breast:
2	chr12:123518174..123520749-chr12:123540012..123542472,2	MCF-7	breast:
3	chr12:123521429..123523174-chr12:123541091..123543118,2	K562	blood:
4	chr12:123519134..123520678-chr12:123539243..123542003,2	K562	blood:
5	chr12:123444883..123447117-chr12:123541287..123543838,2	MCF-7	breast:
6	chr12:123534522..123536134-chr12:123540599..123542732,2	K562	blood:
7	chr12:123527736..123529546-chr12:123540101..123542162,2	K562	blood:
8	chr12:123540726..123542900-chr12:123635050..123636986,3	MCF-7	breast:
9	chr12:123539791..123542781-chr12:123573369..123575868,2	MCF-7	breast:
10	chr12:123527596..123531182-chr12:123539339..123542162,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000090975	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1051434	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs10848428	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11060853	0.95[JPT][hapmap]
rs11608811	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11613937	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12425009	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12425850	1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1568427	0.83[ASW][hapmap]
rs1568428	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap]
rs1615350	0.83[ASW][hapmap];0.83[CHB][hapmap];0.82[TSI][hapmap]
rs1727293	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs1727295	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap]
rs1727302	0.83[CHB][hapmap];0.82[TSI][hapmap]
rs1727307	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1790094	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1790104	1.00[YRI][hapmap]
rs1790106	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1790121	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1790122	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1879379	1.00[ASW][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs1984658	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28755851	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3741530	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3759115	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3897102	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4148862	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4148863	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4148866	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs4275659	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55742290	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs585522	0.80[GIH][hapmap]
rs61955196	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61955214	0.87[ASN][1000 genomes]
rs7135296	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7139321	1.00[YRI][hapmap]
rs7296418	0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7304782	0.83[ASW][hapmap]
rs7305511	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7957096	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]
rs883562	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs884956	1.00[ASW][hapmap];0.95[CHB][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs940904	0.80[GIH][hapmap]
rs949143	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10773921	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs10773921	CDK2AP1	cis	cerebellum	SCAN
rs10773921	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs10773921	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs10773921	PITPNM2	cis	cerebellum	SCAN
rs10773921	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs10773921	TMEM120B	cis	parietal	SCAN
rs10773921	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs10773921	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs10773921	C12orf65	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123519000-123543400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:123528200-123542400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:123528600-123545800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:123529400-123544600	Weak transcription	Small Intestine	intestine
5	chr12:123529600-123546200	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr12:123529800-123548200	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr12:123530800-123544600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr12:123532400-123546600	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr12:123532800-123543400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:123534800-123547200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:123535200-123543000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr12:123535400-123543600	Weak transcription	Spleen	Spleen
13	chr12:123535800-123543200	Weak transcription	Fetal Stomach	stomach
14	chr12:123535800-123543400	Weak transcription	Fetal Intestine Small	intestine
15	chr12:123536000-123544200	Weak transcription	Liver	Liver
16	chr12:123536600-123543400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:123537800-123551200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:123538800-123543800	Genic enhancers	Fetal Thymus	thymus
19	chr12:123538800-123544200	Strong transcription	Primary T cells from cord blood	blood
20	chr12:123539400-123546600	Weak transcription	HSMMtube	muscle
21	chr12:123539600-123546000	Genic enhancers	Thymus	Thymus
22	chr12:123539600-123552600	Enhancers	Right Ventricle	heart
23	chr12:123539800-123549600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr12:123540000-123547200	Weak transcription	NH-A	brain
25	chr12:123540000-123547400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:123540200-123542800	Weak transcription	Fetal Heart	heart
27	chr12:123540200-123543800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:123540400-123543400	Weak transcription	Brain Substantia Nigra	brain
29	chr12:123540400-123544000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:123540600-123541800	Weak transcription	Primary B cells from cord blood	blood
31	chr12:123540600-123543200	Weak transcription	Colon Smooth Muscle	Colon
32	chr12:123540600-123543600	Weak transcription	Fetal Brain Male	brain
33	chr12:123540600-123544000	Weak transcription	Fetal Brain Female	brain
34	chr12:123540600-123547400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:123540800-123543200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:123540800-123543400	Weak transcription	Gastric	stomach
37	chr12:123540800-123543400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr12:123540800-123544000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr12:123541000-123542800	Weak transcription	Brain Anterior Caudate	brain
40	chr12:123541000-123543000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr12:123541000-123543200	Weak transcription	Ovary	ovary
42	chr12:123541000-123543600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr12:123541000-123543800	Weak transcription	Esophagus	oesophagus
44	chr12:123541000-123545200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr12:123541000-123546600	Weak transcription	HepG2	liver
46	chr12:123541200-123542200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr12:123541200-123542600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:123541200-123542600	Weak transcription	Colonic Mucosa	Colon
49	chr12:123541200-123542600	Weak transcription	NHDF-Ad	bronchial
50	chr12:123541200-123542800	Weak transcription	Left Ventricle	heart

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