Variant report

Variant	rs12818179
Chromosome Location	chr12:9852766-9852767
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr12:9852018-9852911	GM12878	blood:	n/a	n/a
2	NFIC	chr12:9852384-9852960	GM12878	blood:	n/a	chr12:9852809-9852825 chr12:9852809-9852826
3	GATA2	chr12:9852560-9852966	HUVEC	blood vessel:	n/a	chr12:9852855-9852872 chr12:9852935-9852942 chr12:9852850-9852866 chr12:9852850-9852866 chr12:9852853-9852863
4	POLR2A	chr12:9849159-9855177	GM12878	blood:	n/a	n/a
5	NFATC1	chr12:9852192-9852787	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:9852207-9853804	GM12891	blood:	n/a	n/a
7	POLR2A	chr12:9852635-9852896	HUVEC	blood vessel:	n/a	n/a
8	REST	chr12:9851876-9853227	H1-neurons	neurons:	n/a	n/a
9	POLR2A	chr12:9852321-9855292	GM19193	blood:	n/a	n/a
10	REST	chr12:9851969-9853374	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9851492..9853618-chr12:9859229..9860813,2	K562	blood:

Variant related genes	Relation type
ENSG00000256582	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1008611	0.83[ASN][1000 genomes]
rs10743821	0.83[ASN][1000 genomes]
rs10743822	0.83[ASN][1000 genomes]
rs10772060	0.89[ASN][1000 genomes]
rs11052718	0.83[ASN][1000 genomes]
rs11052785	0.83[ASN][1000 genomes]
rs12369995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12370579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12371503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12371981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12371982	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12578698	0.83[ASN][1000 genomes]
rs12582616	0.83[ASN][1000 genomes]
rs12809752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12812783	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12814560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12816660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12817550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12817743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12819865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12820674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12823653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12830448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12830867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12830878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1861089	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1990533	0.83[ASN][1000 genomes]
rs2080207	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2192433	0.83[ASN][1000 genomes]
rs2192434	0.83[ASN][1000 genomes]
rs2192435	0.83[ASN][1000 genomes]
rs2192439	0.89[ASN][1000 genomes]
rs2401396	0.83[ASN][1000 genomes]
rs34201389	0.83[ASN][1000 genomes]
rs34623781	0.89[ASN][1000 genomes]
rs34826829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35078787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35512621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763280	1.00[ASN][1000 genomes]
rs4763814	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4763819	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4763835	0.83[ASN][1000 genomes]
rs61913428	0.83[ASN][1000 genomes]
rs66725265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67429242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71441764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7485402	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7954062	0.89[ASN][1000 genomes]
rs7961812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961903	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7974554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975865	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs982511	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
2	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv983235	chr12:9852218-9893776	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12818179	LOC374443	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9826800-9854400	Weak transcription	Esophagus	oesophagus
2	chr12:9827000-9853200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr12:9838800-9854400	Weak transcription	Spleen	Spleen
4	chr12:9839000-9854400	Weak transcription	Lung	lung
5	chr12:9839400-9854600	Weak transcription	Small Intestine	intestine
6	chr12:9840600-9864600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:9841800-9854800	Weak transcription	Right Ventricle	heart
8	chr12:9841800-9863200	Weak transcription	HSMMtube	muscle
9	chr12:9844200-9860600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:9847600-9860000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr12:9848200-9860200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:9848400-9853000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr12:9848400-9854000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr12:9848400-9860200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr12:9848600-9859400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:9849400-9853000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr12:9849400-9853200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr12:9849400-9854000	Weak transcription	Thymus	Thymus
19	chr12:9849800-9853200	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr12:9849800-9854000	Weak transcription	Fetal Thymus	thymus
21	chr12:9849800-9860600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:9850000-9854400	Weak transcription	Left Ventricle	heart
23	chr12:9850200-9854200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:9850400-9854400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr12:9850400-9854600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:9850800-9853400	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr12:9851000-9853400	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr12:9851200-9852800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr12:9851200-9854600	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr12:9851400-9853200	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr12:9851400-9853200	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr12:9851400-9854400	Enhancers	Primary T cells from cord blood	blood
33	chr12:9851600-9852800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:9851600-9852800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:9851800-9853600	Enhancers	HUVEC	blood vessel
36	chr12:9852000-9852800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:9852200-9852800	Enhancers	GM12878-XiMat	blood
38	chr12:9852200-9853000	Genic enhancers	Primary B cells from cord blood	blood
39	chr12:9852200-9854200	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr12:9852200-9854400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr12:9852200-9856400	Enhancers	Primary B cells from peripheral blood	blood
42	chr12:9852400-9852800	Flanking Active TSS	Fetal Heart	heart
43	chr12:9852400-9852800	Enhancers	NHLF	lung
44	chr12:9852400-9853400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:9852400-9855000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr12:9852400-9855600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr12:9852600-9852800	Enhancers	Dnd41	blood
48	chr12:9852600-9853000	Weak transcription	Colon Smooth Muscle	Colon
49	chr12:9852600-9853200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:9852600-9853200	Weak transcription	Rectal Mucosa Donor 29	rectum

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