Variant report

Variant	rs10773001
Chromosome Location	chr12:123741200-123741201
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123716155..123719079-chr12:123740733..123744668,4	K562	blood:
2	chr12:123738852..123742382-chr12:123742428..123743998,3	MCF-7	breast:
3	chr12:123733760..123735468-chr12:123740461..123742402,2	K562	blood:
4	chr12:123740880..123744807-chr12:123747455..123750621,4	MCF-7	breast:
5	chr12:123716188..123719079-chr12:123740733..123744668,4	K562	blood:

Variant related genes	Relation type
ENSG00000130921	Chromatin interaction
ENSG00000051825	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10732573	0.81[EUR][1000 genomes]
rs10734901	0.81[EUR][1000 genomes]
rs10744149	0.83[AMR][1000 genomes]
rs10772995	0.82[AMR][1000 genomes]
rs10772996	0.81[AFR][1000 genomes]
rs10772998	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10773002	0.80[EUR][1000 genomes]
rs10846478	0.83[AMR][1000 genomes]
rs10846486	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10846487	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10846491	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11057192	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11057204	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11057206	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11057210	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12817892	0.88[EUR][1000 genomes]
rs12818067	0.88[EUR][1000 genomes]
rs12824957	0.93[EUR][1000 genomes]
rs12829456	0.88[EUR][1000 genomes]
rs1402274	0.81[AMR][1000 genomes]
rs1402275	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1533703	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1568427	0.83[EUR][1000 genomes]
rs1615694	0.83[AMR][1000 genomes]
rs1626899	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1630693	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1630905	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1716156	0.84[AMR][1000 genomes]
rs1716157	0.83[AMR][1000 genomes]
rs1716159	0.82[AMR][1000 genomes]
rs1716160	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1716164	0.82[AMR][1000 genomes]
rs1716170	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1716171	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1716172	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1716173	0.82[AMR][1000 genomes]
rs1716175	0.82[AMR][1000 genomes]
rs1716176	0.81[AMR][1000 genomes]
rs1716177	0.81[AMR][1000 genomes]
rs1716182	0.81[AMR][1000 genomes]
rs1727290	0.81[AMR][1000 genomes]
rs1727300	0.82[AMR][1000 genomes]
rs1727306	0.82[AMR][1000 genomes]
rs1727320	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1727323	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1727325	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1727334	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1790086	0.83[AMR][1000 genomes]
rs1790087	0.83[AMR][1000 genomes]
rs1790089	0.81[AMR][1000 genomes]
rs1790095	0.81[AMR][1000 genomes]
rs1790098	0.81[AMR][1000 genomes]
rs1790100	0.81[AMR][1000 genomes]
rs1790101	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1790102	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1790124	0.82[AMR][1000 genomes]
rs1790130	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1790131	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1879380	0.96[EUR][1000 genomes]
rs1969354	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1969355	0.83[EUR][1000 genomes]
rs1980251	0.81[EUR][1000 genomes]
rs1980252	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2049114	0.82[AMR][1000 genomes]
rs2337934	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2682430	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2682431	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2682434	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2851435	0.81[EUR][1000 genomes]
rs2851436	0.82[AMR][1000 genomes]
rs2851450	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2851451	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2950537	0.81[AMR][1000 genomes]
rs3018098	0.81[AMR][1000 genomes]
rs34341465	0.88[EUR][1000 genomes]
rs4268544	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4372492	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4759371	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4759409	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4759415	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4759416	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4759417	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58809476	0.88[EUR][1000 genomes]
rs6633	0.94[EUR][1000 genomes]
rs7313483	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7953929	0.89[EUR][1000 genomes]
rs941305	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs941306	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9795522	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[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	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv1803368	chr12:123640853-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	esv1830566	chr12:123640853-123822503	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	esv1836043	chr12:123709409-123822503	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10773001	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs10773001	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs10773001	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs10773001	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs10773001	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs10773001	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs10773001	RP11-282O18.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123725800-123746400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:123733400-123745000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:123734600-123753200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:123735200-123751800	Strong transcription	Fetal Stomach	stomach
5	chr12:123735400-123745400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:123735600-123743400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr12:123735600-123752400	Strong transcription	Thymus	Thymus
8	chr12:123736000-123745400	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr12:123736000-123747800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:123736000-123748000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:123736000-123752200	Strong transcription	Dnd41	blood
12	chr12:123736200-123742400	Strong transcription	Fetal Thymus	thymus
13	chr12:123736200-123744200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr12:123736200-123751400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr12:123736400-123750600	Strong transcription	Fetal Lung	lung
16	chr12:123736400-123752200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:123736400-123752600	Strong transcription	NHLF	lung
18	chr12:123737000-123744000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr12:123737000-123753000	Strong transcription	Fetal Intestine Small	intestine
20	chr12:123737200-123752000	Strong transcription	A549	lung
21	chr12:123737400-123749000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:123737800-123741400	Strong transcription	Colonic Mucosa	Colon
23	chr12:123737800-123742000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:123737800-123743800	Strong transcription	GM12878-XiMat	blood
25	chr12:123737800-123745000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:123737800-123745600	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr12:123737800-123746800	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr12:123738000-123742600	Strong transcription	HepG2	liver
29	chr12:123738000-123743400	Strong transcription	Primary B cells from peripheral blood	blood
30	chr12:123738000-123743400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:123738000-123743600	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr12:123738000-123743600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr12:123738000-123743800	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr12:123738000-123743800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:123738000-123744000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr12:123738000-123744600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:123738000-123745200	Strong transcription	Spleen	Spleen
38	chr12:123738000-123746000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr12:123738000-123746200	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr12:123738000-123746200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr12:123738000-123746600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:123738000-123748200	Strong transcription	Primary T cells from cord blood	blood
43	chr12:123738000-123749200	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr12:123738000-123749200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:123738000-123749600	Strong transcription	Fetal Muscle Leg	muscle
46	chr12:123738000-123749600	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr12:123738000-123750400	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr12:123738000-123751000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr12:123738000-123751200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:123738000-123751800	Strong transcription	Liver	Liver

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