Variant report

Variant	rs1491941
Chromosome Location	chr12:40620815-40620816
allele	C/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	SP1	chr12:40619962-40620942	A549	lung:	n/a	n/a
2	RCOR1	chr12:40619571-40620834	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:40620137-40621088	PFSK-1	brain:	n/a	n/a
4	CREB1	chr12:40620485-40620823	A549	lung:	n/a	n/a
5	EBF1	chr12:40619613-40620945	GM12878	blood:	n/a	chr12:40620810-40620819
6	RELA	chr12:40619964-40621083	GM19099	blood:	n/a	n/a
7	POLR2A	chr12:40616780-40621231	GM18951	blood:	n/a	n/a
8	POLR2A	chr12:40617283-40620948	GM18526	blood:	n/a	n/a
9	JUND	chr12:40620460-40620918	A549	lung:	n/a	chr12:40620464-40620476 chr12:40620581-40620590 chr12:40620580-40620590 chr12:40620580-40620590 chr12:40620579-40620590
10	FOS	chr12:40620406-40620853	MCF10A-Er-Src	breast:	n/a	chr12:40620464-40620476 chr12:40620581-40620590 chr12:40620580-40620590 chr12:40620580-40620590 chr12:40620579-40620590
11	TAL1	chr12:40620623-40620940	K562	blood:	n/a	chr12:40620774-40620792
12	REST	chr12:40619923-40620965	A549	lung:	n/a	n/a
13	TAF1	chr12:40620125-40620863	PFSK-1	brain:	n/a	n/a
14	FOSL2	chr12:40620451-40620852	SK-N-SH	brain:	n/a	chr12:40620464-40620476 chr12:40620581-40620590 chr12:40620580-40620590 chr12:40620580-40620590
15	FOSL2	chr12:40619929-40620993	A549	lung:	n/a	chr12:40620149-40620158 chr12:40620464-40620476 chr12:40620212-40620219 chr12:40620581-40620590 chr12:40620580-40620590 chr12:40620580-40620590
16	EGR1	chr12:40620577-40620834	K562	blood:	n/a	n/a
17	POLR2A	chr12:40620452-40621168	MCF10A-Er-Src	breast:	n/a	n/a
18	JUND	chr12:40620433-40620849	A549	lung:	n/a	chr12:40620464-40620476 chr12:40620581-40620590 chr12:40620580-40620590 chr12:40620580-40620590 chr12:40620579-40620590
19	MAX	chr12:40620102-40620829	A549	lung:	n/a	n/a
20	POLR2A	chr12:40616564-40621335	GM19099	blood:	n/a	n/a
21	GATA2	chr12:40620109-40620840	HUVEC	blood vessel:	n/a	chr12:40620785-40620792 chr12:40620781-40620794 chr12:40620774-40620791
22	TCF12	chr12:40619934-40620982	A549	lung:	n/a	n/a
23	NR3C1	chr12:40620490-40620845	A549	lung:	n/a	n/a
24	POLR2A	chr12:40620479-40620961	PFSK-1	brain:	n/a	n/a
25	MXI1	chr12:40619871-40620851	GM12878	blood:	n/a	n/a
26	TEAD4	chr12:40620617-40620901	K562	blood:	n/a	n/a
27	SP1	chr12:40619921-40620847	A549	lung:	n/a	n/a
28	POLR2A	chr12:40617353-40620863	GM15510	blood:	n/a	n/a
29	WRNIP1	chr12:40620606-40620831	GM12878	blood:	n/a	n/a
30	POLR2A	chr12:40618475-40620954	GM12878	blood:	n/a	n/a
31	MAX	chr12:40620095-40621012	A549	lung:	n/a	n/a
32	POLR2A	chr12:40620639-40620839	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr12:40616903-40621176	GM19193	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40615913..40618239-chr12:40619276..40621204,2	K562	blood:

Variant related genes	Relation type
ENSG00000225342	TF binding region
ENSG00000225342	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1388594	0.83[ASN][1000 genomes]
rs1491932	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1491940	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2131086	0.82[ASN][1000 genomes]
rs2201141	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2263419	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2263420	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2279535	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2638229	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2638230	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2638233	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2638272	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708418	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2708419	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2708420	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2708422	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2708424	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2708427	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2708435	0.86[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2723259	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2723261	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4567538	0.91[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57944060	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7970326	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7973254	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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	nsv1044685	chr12:40574460-40771612	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1052661	chr12:40603049-40642812	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
3	nsv1045408	chr12:40620554-40664424	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40616000-40621200	Active TSS	Primary monocytes fromperipheralblood	blood
2	chr12:40616600-40621000	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr12:40617400-40621000	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr12:40617400-40621000	Active TSS	Right Atrium	heart
5	chr12:40617400-40621400	Active TSS	Aorta	Aorta
6	chr12:40617800-40621000	Active TSS	Rectal Smooth Muscle	rectum
7	chr12:40618000-40621000	Active TSS	A549	lung
8	chr12:40618800-40621200	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr12:40619000-40621000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:40619000-40621000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
11	chr12:40619200-40621200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
12	chr12:40619400-40621000	Enhancers	HUVEC	blood vessel
13	chr12:40619400-40634600	Weak transcription	Spleen	Spleen
14	chr12:40619400-40644400	Weak transcription	Gastric	stomach
15	chr12:40619600-40621000	Enhancers	HMEC	breast
16	chr12:40619600-40621000	Enhancers	NHEK	skin
17	chr12:40619600-40621000	Enhancers	Osteobl	bone
18	chr12:40619600-40636400	Weak transcription	Fetal Muscle Leg	muscle
19	chr12:40619600-40661000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr12:40619600-40678400	Weak transcription	Right Ventricle	heart
21	chr12:40619800-40658800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr12:40620000-40621000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:40620000-40621000	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr12:40620200-40621000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:40620200-40621000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr12:40620200-40621000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:40620200-40621000	Active TSS	Monocytes-CD14+_RO01746	blood
28	chr12:40620200-40621400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:40620400-40621000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
30	chr12:40620400-40621000	Enhancers	Hela-S3	cervix
31	chr12:40620400-40621600	Active TSS	Primary hematopoietic stem cells	blood
32	chr12:40620400-40622600	Weak transcription	Psoas Muscle	Psoas
33	chr12:40620400-40630000	Weak transcription	Ovary	ovary
34	chr12:40620400-40644200	Weak transcription	Brain Angular Gyrus	brain
35	chr12:40620600-40621000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:40620600-40621000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr12:40620600-40621000	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr12:40620600-40621000	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr12:40620600-40621000	Flanking Active TSS	NHDF-Ad	bronchial
40	chr12:40620600-40621000	Flanking Active TSS	NHLF	lung
41	chr12:40620600-40621200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:40620800-40621000	Enhancers	Primary B cells from peripheral blood	blood
43	chr12:40620800-40621000	Enhancers	GM12878-XiMat	blood
44	chr12:40620800-40621000	Enhancers	HSMM	muscle
45	chr12:40620800-40621400	Enhancers	Liver	Liver
46	chr12:40620800-40621400	Active TSS	Fetal Kidney	kidney
47	chr12:40620800-40622400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr12:40620800-40622400	Weak transcription	Colon Smooth Muscle	Colon
49	chr12:40620800-40622600	Weak transcription	Left Ventricle	heart
50	chr12:40620800-40623800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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