Variant report

Variant	rs2073489
Chromosome Location	chr1:227063671-227063672
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	MAFK	chr1:227063328-227063696	HepG2	liver:	n/a	chr1:227063469-227063484 chr1:227063470-227063481 chr1:227063672-227063687 chr1:227063522-227063542 chr1:227063531-227063542 chr1:227063472-227063489
2	FOSL1	chr1:227063552-227064041	K562	blood:	n/a	chr1:227063805-227063816 chr1:227063809-227063817 chr1:227063807-227063819 chr1:227063781-227063792
3	POLR2A	chr1:227063535-227063875	MCF10A-Er-Src	breast:	n/a	n/a
4	JUN	chr1:227063225-227064640	K562	blood:	n/a	chr1:227063805-227063816 chr1:227063809-227063817 chr1:227063807-227063819 chr1:227063781-227063792 chr1:227064566-227064576 chr1:227064105-227064114
5	JUND	chr1:227063598-227064014	K562	blood:	n/a	chr1:227063805-227063816 chr1:227063809-227063817 chr1:227063807-227063819 chr1:227063781-227063792
6	BHLHE40	chr1:227063546-227064039	K562	blood:	n/a	n/a
7	TBL1XR1	chr1:227063616-227063882	K562	blood:	n/a	n/a
8	FOS	chr1:227063447-227064027	MCF10A-Er-Src	breast:	n/a	chr1:227063805-227063816 chr1:227063809-227063817 chr1:227063807-227063819 chr1:227063781-227063792
9	RCOR1	chr1:227063527-227063941	K562	blood:	n/a	n/a
10	CREB1	chr1:227063488-227064095	K562	blood:	n/a	n/a
11	MAFK	chr1:227063342-227063925	K562	blood:	n/a	chr1:227063469-227063484 chr1:227063470-227063481 chr1:227063672-227063687 chr1:227063522-227063542 chr1:227063531-227063542 chr1:227063472-227063489
12	FOSL2	chr1:227063547-227064090	A549	lung:	n/a	chr1:227063805-227063816 chr1:227063809-227063817 chr1:227063807-227063819 chr1:227063781-227063792
13	CREB1	chr1:227063606-227064014	H1-hESC	embryonic stem cell:	n/a	n/a
14	MYC	chr1:227063652-227063961	MCF10A-Er-Src	breast:	n/a	n/a
15	SPI1	chr1:227063530-227063756	K562	blood:	n/a	chr1:227063676-227063689
16	ELF1	chr1:227063432-227063987	K562	blood:	n/a	chr1:227063675-227063688
17	ATF3	chr1:227063633-227064029	K562	blood:	n/a	n/a
18	CREB1	chr1:227063607-227063991	A549	lung:	n/a	n/a
19	JUND	chr1:227063617-227063960	A549	lung:	n/a	chr1:227063805-227063816 chr1:227063809-227063817 chr1:227063807-227063819 chr1:227063781-227063792
20	FOS	chr1:227063447-227063982	MCF10A-Er-Src	breast:	n/a	chr1:227063805-227063816 chr1:227063809-227063817 chr1:227063807-227063819 chr1:227063781-227063792
21	MAFK	chr1:227063368-227063856	H1-hESC	embryonic stem cell:	n/a	chr1:227063469-227063484 chr1:227063470-227063481 chr1:227063672-227063687 chr1:227063522-227063542 chr1:227063531-227063542 chr1:227063472-227063489
22	STAT3	chr1:227063566-227063884	MCF10A-Er-Src	breast:	n/a	chr1:227063786-227063798
23	JUND	chr1:227063603-227063920	H1-hESC	embryonic stem cell:	n/a	chr1:227063805-227063816 chr1:227063809-227063817 chr1:227063807-227063819 chr1:227063781-227063792
24	POLR2A	chr1:227063519-227063989	HCT-116	colon:	n/a	n/a
25	POLR2A	chr1:227063515-227063977	HCT-116	colon:	n/a	n/a
26	BACH1	chr1:227063473-227063904	H1-hESC	embryonic stem cell:	n/a	chr1:227063806-227063820
27	FOS	chr1:227063649-227063989	MCF10A-Er-Src	breast:	n/a	chr1:227063805-227063816 chr1:227063809-227063817 chr1:227063807-227063819 chr1:227063781-227063792
28	MAZ	chr1:227063586-227064026	K562	blood:	n/a	n/a
29	FOSL2	chr1:227063652-227063946	A549	lung:	n/a	chr1:227063805-227063816 chr1:227063809-227063817 chr1:227063807-227063819 chr1:227063781-227063792
30	IRF1	chr1:227063616-227063988	K562	blood:	n/a	chr1:227063787-227063801
31	ATF1	chr1:227063668-227063972	K562	blood:	n/a	n/a
32	CBX3	chr1:227063466-227064059	K562	blood:	n/a	n/a
33	MAFF	chr1:227063427-227063685	HepG2	liver:	n/a	n/a
34	NR2F2	chr1:227063447-227064116	K562	blood:	n/a	n/a
35	POLR2A	chr1:227063600-227063698	MCF-7	breast:	n/a	n/a
36	RCOR1	chr1:227063536-227064020	K562	blood:	n/a	n/a
37	FOS	chr1:227063632-227063992	MCF10A-Er-Src	breast:	n/a	chr1:227063805-227063816 chr1:227063809-227063817 chr1:227063807-227063819 chr1:227063781-227063792
38	CUX1	chr1:227063523-227063715	K562	blood:	n/a	n/a
39	MAX	chr1:227063624-227064126	K562	blood:	n/a	n/a
40	JUN	chr1:227063612-227064043	K562	blood:	n/a	chr1:227063805-227063816 chr1:227063809-227063817 chr1:227063807-227063819 chr1:227063781-227063792

No.	Distal block	Cell Line	Cell type
1	chr1:227056972..227060781-chr1:227061022..227064648,10	MCF-7	breast:
2	chr1:227061527..227064235-chr1:227072734..227074353,2	K562	blood:
3	chr1:227057812..227060402-chr1:227061799..227065310,4	MCF-7	breast:
4	chr1:227062873..227064895-chr1:227127991..227129793,2	K562	blood:
5	chr1:227063385..227063950-chr11:76463692..76464295,2	Hela-S3	cervix:

Variant related genes	Relation type
PSEN2	TF binding region
ENSG00000163050	Chromatin interaction
ENSG00000143801	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1046240	0.95[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs1150897	0.93[ASN][1000 genomes]
rs1150900	0.90[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs11802358	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12086302	0.87[ASN][1000 genomes]
rs1295638	0.95[CHB][hapmap];0.86[JPT][hapmap];0.98[ASN][1000 genomes]
rs1295640	0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap]
rs1295641	0.98[ASN][1000 genomes]
rs1295643	0.98[ASN][1000 genomes]
rs1295647	0.90[ASN][1000 genomes]
rs1296171	0.91[ASN][1000 genomes]
rs2236914	0.90[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2236915	0.90[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2793461	0.98[ASN][1000 genomes]
rs2802268	0.83[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.92[LWK][hapmap];0.92[ASN][1000 genomes]
rs2855559	0.90[ASN][1000 genomes]
rs2855560	0.90[ASN][1000 genomes]
rs2855564	0.89[ASN][1000 genomes]
rs4653470	0.94[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs6426541	0.81[ASN][1000 genomes]
rs6426547	0.88[ASN][1000 genomes]
rs6426548	0.89[ASN][1000 genomes]
rs6674701	0.89[ASN][1000 genomes]
rs6688068	0.89[ASN][1000 genomes]
rs6692729	0.89[ASN][1000 genomes]
rs6697001	0.89[ASN][1000 genomes]
rs6697431	0.89[ASN][1000 genomes]
rs6759	0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.98[ASN][1000 genomes]
rs7514364	0.89[ASN][1000 genomes]
rs7518926	0.88[ASN][1000 genomes]
rs7530245	0.88[ASN][1000 genomes]
rs7530370	0.91[ASN][1000 genomes]
rs7547071	0.89[ASN][1000 genomes]
rs8383	0.90[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	nsv4766	chr1:227025954-227070961	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2073489	PSEN2	cis	lymphoblastoid	seeQTL
rs2073489	SUSD4	cis	parietal	SCAN
rs2073489	C1orf95	cis	cerebellum	SCAN
rs2073489	ARF1	cis	cerebellum	SCAN
rs2073489	PARP1	cis	cerebellum	SCAN
rs2073489	LEFTY1	cis	cerebellum	SCAN
rs2073489	PSEN2	cis	cerebellum	SCAN
rs2073489	CABC1	cis	cerebellum	SCAN
rs2073489	HIST3H2BB	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227059000-227066800	Weak transcription	Aorta	Aorta
2	chr1:227059200-227069000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr1:227059400-227069600	Weak transcription	Primary B cells from cord blood	blood
4	chr1:227059600-227066000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:227059600-227068400	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:227059600-227069200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:227059600-227070200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:227059800-227064400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:227059800-227064400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr1:227059800-227064600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr1:227059800-227064600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr1:227059800-227064600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:227059800-227065000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:227059800-227067400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:227059800-227070200	Weak transcription	Osteobl	bone
16	chr1:227059800-227075600	Weak transcription	Brain Substantia Nigra	brain
17	chr1:227059800-227095000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:227060000-227063800	Weak transcription	Brain Anterior Caudate	brain
19	chr1:227060000-227064600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:227060000-227064600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:227060000-227064600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:227060000-227065000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:227060000-227065000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:227060000-227065000	Weak transcription	HMEC	breast
25	chr1:227060000-227068200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:227060000-227068200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:227060000-227068400	Weak transcription	Brain Angular Gyrus	brain
28	chr1:227060000-227068800	Weak transcription	NHDF-Ad	bronchial
29	chr1:227060000-227069400	Weak transcription	Esophagus	oesophagus
30	chr1:227060000-227069600	Weak transcription	Right Atrium	heart
31	chr1:227060000-227069800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr1:227060000-227070000	Weak transcription	Small Intestine	intestine
33	chr1:227060000-227070600	Weak transcription	Fetal Brain Male	brain
34	chr1:227060200-227070200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:227060400-227066200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:227060400-227067000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr1:227060400-227068400	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:227060400-227069200	Weak transcription	GM12878-XiMat	blood
39	chr1:227060400-227073800	Weak transcription	HepG2	liver
40	chr1:227060400-227077600	Weak transcription	Brain Germinal Matrix	brain
41	chr1:227060600-227064200	Weak transcription	Adipose Nuclei	Adipose
42	chr1:227060600-227065000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:227060600-227067200	Weak transcription	Ovary	ovary
44	chr1:227060600-227067400	Weak transcription	NHLF	lung
45	chr1:227060600-227068400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:227060600-227070400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr1:227060600-227070400	Weak transcription	HUVEC	blood vessel
48	chr1:227060600-227077400	Weak transcription	Fetal Brain Female	brain
49	chr1:227061200-227069800	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr1:227061600-227063800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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