Variant report

Variant	rs12830878
Chromosome Location	chr12:9854415-9854416
allele	A/G
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	POLR2A	chr12:9854385-9855159	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr12:9854325-9855350	GM12878	blood:	n/a	n/a
3	MTA3	chr12:9853995-9855294	GM12878	blood:	n/a	n/a
4	EBF1	chr12:9854354-9854723	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:9849159-9855177	GM12878	blood:	n/a	n/a
6	RELA	chr12:9854340-9855184	GM19099	blood:	n/a	n/a
7	FOXA2	chr12:9854327-9854619	A549	lung:	n/a	n/a
8	POLR2A	chr12:9854364-9855222	GM12878	blood:	n/a	n/a
9	FOXA2	chr12:9854333-9854694	A549	lung:	n/a	n/a
10	POLR2A	chr12:9854412-9854758	GM12878	blood:	n/a	n/a
11	POLR2A	chr12:9852321-9855292	GM19193	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9853903..9855741-chr12:9860997..9863949,2	MCF-7	breast:
2	chr12:9799499..9803059-chr12:9853903..9856114,3	K562	blood:

Variant related genes	Relation type
ENSG00000256582	TF binding region
ENSG00000256442	Chromatin interaction
ENSG00000256594	Chromatin interaction

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]
rs12818179	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]
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
rs12830878	LOC374443	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9839400-9854600	Weak transcription	Small Intestine	intestine
2	chr12:9840600-9864600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:9841800-9854800	Weak transcription	Right Ventricle	heart
4	chr12:9841800-9863200	Weak transcription	HSMMtube	muscle
5	chr12:9844200-9860600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:9847600-9860000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr12:9848200-9860200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:9848400-9860200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr12:9848600-9859400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:9849800-9860600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:9850400-9854600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:9851200-9854600	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr12:9852200-9856400	Enhancers	Primary B cells from peripheral blood	blood
14	chr12:9852400-9855000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr12:9852400-9855600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr12:9852600-9856600	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr12:9853000-9854600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:9853000-9856200	Enhancers	Primary B cells from cord blood	blood
19	chr12:9853200-9854600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr12:9853200-9854600	Enhancers	GM12878-XiMat	blood
21	chr12:9853400-9858400	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr12:9853400-9858400	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr12:9853800-9854600	Enhancers	Primary T cells fromperipheralblood	blood
24	chr12:9854000-9854600	Enhancers	Fetal Thymus	thymus
25	chr12:9854000-9854600	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr12:9854000-9854600	Enhancers	Thymus	Thymus
27	chr12:9854200-9855200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr12:9854200-9855600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr12:9854200-9855600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:9854200-9855800	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr12:9854400-9854600	Enhancers	Left Ventricle	heart
32	chr12:9854400-9854600	Enhancers	Lung	lung
33	chr12:9854400-9854800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr12:9854400-9854800	ZNF genes & repeats	Spleen	Spleen
35	chr12:9854400-9855000	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr12:9854400-9855200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr12:9854400-9855200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
38	chr12:9854400-9855200	ZNF genes & repeats	Esophagus	oesophagus
39	chr12:9854400-9855400	Flanking Active TSS	Dnd41	blood
40	chr12:9854400-9855600	Enhancers	Primary hematopoietic stem cells	blood
41	chr12:9854400-9855600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:9854400-9855600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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