Variant report

Variant	rs591992
Chromosome Location	chr12:121019323-121019324
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	chr12:121018751-121019568	GM12892	blood:	n/a	n/a
2	POLR2A	chr12:121018701-121019655	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:121018811-121019611	MCF-7	breast:	n/a	n/a
4	MAX	chr12:121018986-121019473	H1-hESC	embryonic stem cell:	n/a	n/a
5	REST	chr12:121018620-121019790	H1-neurons	neurons:	n/a	n/a
6	FOSL2	chr12:121018791-121019790	A549	lung:	n/a	chr12:121019222-121019231
7	POLR2A	chr12:121017912-121019735	PANC-1	pancreas:	n/a	n/a
8	YY1	chr12:121018804-121019601	SK-N-SH	brain:	n/a	chr12:121019063-121019074
9	GABPA	chr12:121018689-121019647	A549	lung:	n/a	chr12:121019350-121019364 chr12:121019353-121019364 chr12:121019353-121019362
10	JUND	chr12:121018543-121020214	SK-N-SH	brain:	n/a	chr12:121019222-121019231
11	SIN3A	chr12:121018596-121019768	H1-hESC	embryonic stem cell:	n/a	n/a
12	YY1	chr12:121018742-121019477	K562	blood:	n/a	chr12:121019063-121019074
13	RELA	chr12:121018969-121019652	GM19099	blood:	n/a	n/a
14	ZMIZ1	chr12:121018971-121019660	K562	blood:	n/a	n/a
15	POLR2A	chr12:121018127-121019643	PANC-1	pancreas:	n/a	n/a
16	TBL1XR1	chr12:121018982-121019328	GM12878	blood:	n/a	n/a
17	CTCF	chr12:121019275-121019373	Lung_OC	lung:	n/a	n/a
18	YY1	chr12:121018735-121019565	A549	lung:	n/a	chr12:121019063-121019074
19	POLR2A	chr12:121016717-121019832	SK-N-MC	brain:	n/a	n/a
20	BCLAF1	chr12:121018810-121019652	GM12878	blood:	n/a	n/a
21	ETS1	chr12:121018753-121019580	A549	lung:	n/a	chr12:121019199-121019208 chr12:121019199-121019208 chr12:121019199-121019208 chr12:121019199-121019208 chr12:121019196-121019211 chr12:121019195-121019211
22	POLR2A	chr12:121018805-121019612	GM18526	blood:	n/a	n/a
23	TCF7L2	chr12:121018992-121019394	PANC-1	pancreas:	n/a	n/a
24	YY1	chr12:121018721-121019565	GM12878	blood:	n/a	chr12:121019063-121019074
25	CCNT2	chr12:121018784-121019422	K562	blood:	n/a	n/a
26	ELF1	chr12:121018964-121019406	A549	lung:	n/a	chr12:121019197-121019208
27	RUNX3	chr12:121018814-121019608	GM12878	blood:	n/a	n/a
28	TBP	chr12:121018968-121019612	HepG2	liver:	n/a	n/a
29	POLR2A	chr12:121018746-121019589	A549	lung:	n/a	n/a
30	SP1	chr12:121018949-121019579	GM12878	blood:	n/a	chr12:121019329-121019339 chr12:121019329-121019338
31	MBD4	chr12:121018952-121019543	HepG2	liver:	n/a	n/a
32	FOXA1	chr12:121019061-121019600	T-47D	breast:	n/a	n/a
33	POLR2A	chr12:121018956-121019521	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr12:121018612-121019590	K562	blood:	n/a	n/a
35	MXI1	chr12:121018832-121019600	Hela-S3	cervix:	n/a	n/a
36	PAX5	chr12:121018946-121019567	GM12878	blood:	n/a	n/a
37	YY1	chr12:121018762-121019548	HepG2	liver:	n/a	chr12:121019063-121019074
38	POLR2A	chr12:121018713-121019591	GM12878	blood:	n/a	n/a
39	SIX5	chr12:121018349-121019593	A549	lung:	n/a	n/a
40	TAF1	chr12:121018806-121019402	GM12892	blood:	n/a	n/a
41	BHLHE40	chr12:121018856-121019501	K562	blood:	n/a	n/a
42	POLR2A	chr12:121018795-121019710	H1-neurons	neurons:	n/a	n/a
43	POLR2A	chr12:121017993-121019705	MCF-7	breast:	n/a	n/a
44	NFYB	chr12:121019003-121019454	Hela-S3	cervix:	n/a	n/a
45	NFYA	chr12:121019070-121019441	GM12878	blood:	n/a	chr12:121019218-121019236
46	GABPA	chr12:121018666-121019636	MCF-7	breast:	n/a	chr12:121019350-121019364 chr12:121019353-121019364 chr12:121019353-121019362
47	CEBPD	chr12:121018908-121019523	HepG2	liver:	n/a	n/a
48	POLR2A	chr12:121018884-121019619	SK-N-MC	brain:	n/a	n/a
49	POU2F2	chr12:121018825-121019624	GM12878	blood:	n/a	n/a
50	NFYA	chr12:121018958-121019472	Hela-S3	cervix:	n/a	chr12:121019218-121019236

No.	Distal block	Cell Line	Cell type
1	chr12:121018631..121021385-chr12:121124185..121125689,2	MCF-7	breast:
2	chr12:120970635..120973356-chr12:121018386..121020894,3	K562	blood:
3	chr12:120905819..120908222-chr12:121018300..121020103,2	MCF-7	breast:
4	chr12:120971743..120974059-chr12:121017467..121020168,3	MCF-7	breast:
5	chr12:121017632..121023235-chr12:121123750..121127979,5	K562	blood:
6	chr12:121019025..121020943-chr12:121076838..121078875,3	K562	blood:
7	chr12:120728472..120731126-chr12:121019042..121021642,2	K562	blood:
8	chr12:121002647..121005056-chr12:121017144..121019429,2	MCF-7	breast:
9	chr1:19923267..19923950-chr12:121018737..121019591,2	Hela-S3	cervix:
10	chr12:121018631..121020878-chr12:121162530..121164769,2	MCF-7	breast:
11	chr12:120994023..120996050-chr12:121018061..121019874,2	K562	blood:
12	chr12:120965360..120967085-chr12:121018477..121020344,2	MCF-7	breast:

Variant related genes	Relation type
POP5	TF binding region
ENSG00000088986	Chromatin interaction
ENSG00000110917	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000110871	Chromatin interaction
ENSG00000157782	Chromatin interaction
ENSG00000256008	Chromatin interaction
ENSG00000235185	Chromatin interaction
ENSG00000111786	Chromatin interaction
ENSG00000022840	Chromatin interaction
ENSG00000173436	Chromatin interaction
ENSG00000270136	Chromatin interaction
ENSG00000122971	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10849755	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1167695	0.84[EUR][1000 genomes]
rs1167700	0.87[ASN][1000 genomes]
rs1167703	0.84[ASN][1000 genomes]
rs1167725	0.84[CHB][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1167726	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1167727	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12307148	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12310837	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs1614223	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1622884	0.81[EUR][1000 genomes]
rs1671767	0.81[ASN][1000 genomes]
rs17431717	0.84[CEU][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs1794748	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1794749	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2235222	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2673618	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4347449	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs550876	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs563920	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567156	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs580016	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs588132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs614226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs616157	0.86[EUR][1000 genomes]
rs640350	0.88[EUR][1000 genomes]
rs7137953	0.85[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7174	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73405622	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787824	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs787827	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs787832	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7956998	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7963543	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs7972244	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv973944	chr12:121017088-121027122	Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs591992	COQ5	cis	parietal	SCAN
rs591992	HRK	cis	cerebellum	SCAN
rs591992	POP5	cis	Lymphoblastoid	GTEx
rs591992	POP5	Cis_1M	lymphoblastoid	RTeQTL
rs591992	GCN1L1	cis	cerebellum	SCAN
rs591992	GATC	cis	cerebellum	SCAN
rs591992	POP5	cis	lymphoblastoid	seeQTL
rs591992	POP5	cis	cerebellum	SCAN
rs591992	GATC	cis	lymphoblastoid	seeQTL
rs591992	HIRA	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121017800-121019600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:121018000-121019400	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr12:121018000-121019400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:121018000-121019400	Active TSS	Fetal Kidney	kidney
5	chr12:121018000-121019600	Active TSS	H1 Cell Line	embryonic stem cell
6	chr12:121018000-121019600	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr12:121018000-121019600	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr12:121018000-121020000	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr12:121018200-121019600	Active TSS	H9 Cell Line	embryonic stem cell
10	chr12:121018200-121019800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr12:121018200-121019800	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr12:121018200-121020000	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr12:121018200-121020000	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr12:121018200-121020200	Active TSS	Rectal Smooth Muscle	rectum
15	chr12:121018400-121019400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:121018400-121019400	Active TSS	HMEC	breast
17	chr12:121018400-121019400	Active TSS	HSMM	muscle
18	chr12:121018400-121019400	Active TSS	NH-A	brain
19	chr12:121018400-121019600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr12:121018400-121019600	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr12:121018400-121019800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr12:121018400-121019800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:121018400-121019800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:121018400-121019800	Active TSS	Fetal Intestine Large	intestine
25	chr12:121018400-121019800	Active TSS	Psoas Muscle	Psoas
26	chr12:121018400-121019800	Active TSS	A549	lung
27	chr12:121018400-121019800	Active TSS	HSMMtube	muscle
28	chr12:121018400-121020000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr12:121018400-121020000	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr12:121018400-121020000	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr12:121018400-121020000	Active TSS	Brain Angular Gyrus	brain
32	chr12:121018400-121020000	Active TSS	Colonic Mucosa	Colon
33	chr12:121018400-121020000	Active TSS	GM12878-XiMat	blood
34	chr12:121018400-121020200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr12:121018400-121020200	Active TSS	Thymus	Thymus
36	chr12:121018600-121019400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:121018600-121019400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:121018600-121019400	Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr12:121018600-121019400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:121018600-121019400	Active TSS	Fetal Intestine Small	intestine
41	chr12:121018600-121019400	Active TSS	Fetal Muscle Trunk	muscle
42	chr12:121018600-121019400	Active TSS	Hela-S3	cervix
43	chr12:121018600-121019400	Active TSS	NHEK	skin
44	chr12:121018600-121019400	Active TSS	Osteobl	bone
45	chr12:121018600-121019600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr12:121018600-121019600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:121018600-121019600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:121018600-121019600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:121018600-121019600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr12:121018600-121019600	Active TSS	Primary T helper naive cells from peripheral blood	blood

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