Variant report

Variant	rs9795522
Chromosome Location	chr12:123730935-123730936
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123457645..123460570-chr12:123729103..123732056,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256028	Chromatin interaction
ENSG00000150967	Chromatin interaction
ENSG00000111325	Chromatin interaction

Extended variants
information (count: 149 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:145)

rs_ID	r²[population]
rs1047158	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1051431	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10744148	0.83[AMR][1000 genomes]
rs10744149	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10744150	0.80[EUR][1000 genomes]
rs10744151	0.83[EUR][1000 genomes]
rs10772993	0.82[EUR][1000 genomes]
rs10772995	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10772996	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10772997	0.82[EUR][1000 genomes]
rs10772998	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10772999	0.82[EUR][1000 genomes]
rs10773001	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10846478	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10846486	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10846487	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10846491	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11057192	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11057202	0.82[EUR][1000 genomes]
rs11057204	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11057205	0.82[EUR][1000 genomes]
rs11057206	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11057207	0.83[EUR][1000 genomes]
rs11057209	0.82[EUR][1000 genomes]
rs11057210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1106240	0.81[EUR][1000 genomes]
rs1106241	0.83[EUR][1000 genomes]
rs12817892	0.96[EUR][1000 genomes]
rs12818067	0.96[EUR][1000 genomes]
rs12824957	0.85[EUR][1000 genomes]
rs12829456	0.96[EUR][1000 genomes]
rs1402274	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1402275	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1533703	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1569068	0.83[EUR][1000 genomes]
rs1609520	0.81[EUR][1000 genomes]
rs1615694	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1616131	0.83[EUR][1000 genomes]
rs1616181	0.83[EUR][1000 genomes]
rs1617434	0.83[EUR][1000 genomes]
rs1618679	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1621194	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1626899	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1627724	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1630693	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1630905	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1716156	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1716157	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1716158	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1716159	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1716160	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1716164	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1716165	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1716167	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1716168	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1716169	0.81[EUR][1000 genomes]
rs1716170	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1716171	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1716172	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1716173	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1716175	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1716176	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1716177	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1716182	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1716185	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1727290	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1727294	0.83[EUR][1000 genomes]
rs1727296	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1727300	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1727306	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1727309	0.84[EUR][1000 genomes]
rs1727310	0.84[EUR][1000 genomes]
rs1727313	0.81[EUR][1000 genomes]
rs1727314	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1727315	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1727316	0.83[EUR][1000 genomes]
rs1727320	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1727322	0.83[EUR][1000 genomes]
rs1727323	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1727324	0.87[EUR][1000 genomes]
rs1727325	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1727331	0.81[EUR][1000 genomes]
rs1727332	0.82[EUR][1000 genomes]
rs1727334	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1790086	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1790087	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1790089	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1790090	0.84[EUR][1000 genomes]
rs1790095	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1790098	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1790100	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1790101	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1790102	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1790108	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1790109	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1790116	0.83[EUR][1000 genomes]
rs1790123	0.84[EUR][1000 genomes]
rs1790124	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1790125	0.88[AMR][1000 genomes]
rs1790130	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1790131	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1879380	0.88[EUR][1000 genomes]
rs1969354	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1980252	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2049114	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2337934	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2510885	0.80[EUR][1000 genomes]
rs2682426	0.80[AMR][1000 genomes]
rs2682429	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2682430	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2682431	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2682433	0.88[EUR][1000 genomes]
rs2682434	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2695476	0.88[EUR][1000 genomes]
rs2695478	0.87[EUR][1000 genomes]
rs2695479	0.85[EUR][1000 genomes]
rs2695480	0.87[EUR][1000 genomes]
rs2695481	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2695482	0.83[EUR][1000 genomes]
rs2851435	0.89[EUR][1000 genomes]
rs2851436	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2851438	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2851450	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2851451	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2947099	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2950537	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3018098	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34341465	0.96[EUR][1000 genomes]
rs4268544	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4372492	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4759371	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4759409	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4759415	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4759416	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4759417	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58809476	0.96[EUR][1000 genomes]
rs6633	0.86[EUR][1000 genomes]
rs7137286	0.83[EUR][1000 genomes]
rs7304782	0.81[EUR][1000 genomes]
rs7313483	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7953929	0.81[EUR][1000 genomes]
rs884548	0.84[EUR][1000 genomes]
rs941305	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs941306	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs949142	0.84[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
rs9795522	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs9795522	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs9795522	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs9795522	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs9795522	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs9795522	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs9795522	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123718800-123733000	Weak transcription	Esophagus	oesophagus
2	chr12:123718800-123733800	Weak transcription	Aorta	Aorta
3	chr12:123718800-123739600	Weak transcription	Fetal Kidney	kidney
4	chr12:123719000-123731600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:123719000-123732600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr12:123719000-123735000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:123719200-123733000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:123719200-123735200	Weak transcription	Ovary	ovary
9	chr12:123719600-123734200	Weak transcription	Colonic Mucosa	Colon
10	chr12:123719600-123738400	Weak transcription	NH-A	brain
11	chr12:123719800-123733600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:123719800-123733600	Weak transcription	Spleen	Spleen
13	chr12:123719800-123733800	Weak transcription	Fetal Intestine Large	intestine
14	chr12:123720000-123732800	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr12:123720000-123736000	Weak transcription	Gastric	stomach
16	chr12:123720000-123738000	Weak transcription	Small Intestine	intestine
17	chr12:123720200-123735200	Weak transcription	Pancreas	Pancrea
18	chr12:123720600-123733000	Weak transcription	Fetal Brain Female	brain
19	chr12:123721000-123733800	Weak transcription	Lung	lung
20	chr12:123721600-123735200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr12:123722800-123733600	Weak transcription	Osteobl	bone
22	chr12:123723000-123733000	Weak transcription	Dnd41	blood
23	chr12:123723200-123733000	Weak transcription	NHLF	lung
24	chr12:123723400-123735000	Weak transcription	Stomach Mucosa	stomach
25	chr12:123723600-123733000	Weak transcription	Primary B cells from cord blood	blood
26	chr12:123724400-123733000	Weak transcription	HMEC	breast
27	chr12:123724600-123735200	Weak transcription	Placenta	Placenta
28	chr12:123725200-123738000	Weak transcription	HSMM	muscle
29	chr12:123725800-123746400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr12:123726600-123733000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:123726600-123735200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr12:123727000-123733000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr12:123727000-123733000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:123727000-123735000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:123727200-123732600	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr12:123727200-123732600	Weak transcription	Liver	Liver
37	chr12:123727200-123733000	Weak transcription	Brain Germinal Matrix	brain
38	chr12:123727200-123735000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr12:123727200-123735000	Weak transcription	Brain Hippocampus Middle	brain
40	chr12:123727200-123735000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr12:123727200-123735200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr12:123727400-123731800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr12:123727400-123731800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:123727400-123733000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr12:123727400-123733000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr12:123727400-123733000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr12:123727400-123733000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr12:123727400-123733000	Weak transcription	Fetal Lung	lung
49	chr12:123727400-123733000	Weak transcription	Right Ventricle	heart
50	chr12:123727400-123733800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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