Variant report

Variant	rs1254901
Chromosome Location	chr2:85811229-85811230
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	MAX	chr2:85810379-85813165	HepG2	liver:	n/a	n/a
2	FOXA2	chr2:85810833-85811286	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:85811220-85812452	GM19099	blood:	n/a	n/a
4	POLR2A	chr2:85810906-85812963	HUVEC	blood vessel:	n/a	n/a
5	CEBPB	chr2:85810879-85811252	HepG2	liver:	n/a	chr2:85811094-85811105
6	CREB1	chr2:85810740-85812847	HepG2	liver:	n/a	n/a
7	POLR2A	chr2:85810731-85812788	HepG2	liver:	n/a	n/a
8	POLR2A	chr2:85811185-85812428	GM19193	blood:	n/a	n/a
9	POLR2A	chr2:85811059-85813388	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr2:85810858-85813001	HepG2	liver:	n/a	n/a
11	IRF4	chr2:85811127-85811507	GM12878	blood:	n/a	n/a
12	CEBPB	chr2:85810910-85811286	IMR90	lung:	n/a	chr2:85811094-85811105
13	HNF4G	chr2:85811217-85812607	HepG2	liver:	n/a	chr2:85812366-85812378 chr2:85812366-85812378 chr2:85812365-85812379 chr2:85812539-85812546 chr2:85811685-85811699 chr2:85811685-85811700 chr2:85811685-85811700 chr2:85812534-85812550 chr2:85812364-85812379 chr2:85811686-85811698 chr2:85812363-85812381 chr2:85811685-85811700 chr2:85811686-85811698 chr2:85812366-85812378 chr2:85811683-85811701 chr2:85812365-85812379 chr2:85812366-85812379 chr2:85812365-85812378 chr2:85811686-85811694 chr2:85812366-85812378 chr2:85812365-85812379 chr2:85811685-85811700 chr2:85811685-85811699
14	POLR2A	chr2:85810732-85812739	HepG2	liver:	n/a	n/a
15	MYBL2	chr2:85810791-85812774	HepG2	liver:	n/a	n/a
16	BATF	chr2:85811168-85811531	GM12878	blood:	n/a	n/a
17	CEBPB	chr2:85810955-85811251	K562	blood:	n/a	chr2:85811094-85811105
18	CHD2	chr2:85811116-85811301	HepG2	liver:	n/a	n/a
19	ELF1	chr2:85811101-85812043	GM12878	blood:	n/a	chr2:85811596-85811608 chr2:85811595-85811604
20	POLR2A	chr2:85811141-85812618	GM12878	blood:	n/a	n/a
21	CEBPB	chr2:85810835-85811296	HepG2	liver:	n/a	chr2:85811094-85811105
22	EBF1	chr2:85811178-85811779	GM12878	blood:	n/a	chr2:85811711-85811720
23	POLR2A	chr2:85810732-85811257	HepG2	liver:	n/a	n/a
24	MTA3	chr2:85810979-85812986	GM12878	blood:	n/a	n/a
25	MAZ	chr2:85811152-85811667	GM12878	blood:	n/a	n/a
26	POLR2A	chr2:85811192-85811889	GM18951	blood:	n/a	n/a
27	IRF4	chr2:85811120-85811619	GM12878	blood:	n/a	n/a
28	HDAC2	chr2:85811155-85812710	HepG2	liver:	n/a	chr2:85812248-85812257 chr2:85812557-85812566 chr2:85811827-85811846
29	TEAD4	chr2:85810763-85811414	HepG2	liver:	n/a	n/a
30	POLR2A	chr2:85810799-85812072	GM12878	blood:	n/a	n/a
31	POLR2A	chr2:85810845-85811354	K562	blood:	n/a	n/a
32	POLR2A	chr2:85811068-85812579	GM12892	blood:	n/a	n/a
33	POLR2A	chr2:85811213-85812415	GM12878	blood:	n/a	n/a
34	STAT5A	chr2:85811079-85811488	GM12878	blood:	n/a	n/a
35	CHD2	chr2:85811207-85811349	GM12878	blood:	n/a	n/a
36	REST	chr2:85811215-85812667	HepG2	liver:	n/a	chr2:85811580-85811590 chr2:85811818-85811831 chr2:85811830-85811843 chr2:85811548-85811561 chr2:85811827-85811845 chr2:85811830-85811843
37	HNF4A	chr2:85810795-85812584	HepG2	liver:	n/a	chr2:85812366-85812378 chr2:85812366-85812378 chr2:85812365-85812379 chr2:85812539-85812546 chr2:85811685-85811699 chr2:85811685-85811700 chr2:85811685-85811700 chr2:85812534-85812550 chr2:85812364-85812379 chr2:85811686-85811698 chr2:85812363-85812381 chr2:85811685-85811700 chr2:85811686-85811698 chr2:85812366-85812378 chr2:85811683-85811701 chr2:85812365-85812379 chr2:85812366-85812379 chr2:85812365-85812378 chr2:85811686-85811694 chr2:85812366-85812378 chr2:85812365-85812379 chr2:85811684-85811699 chr2:85812364-85812379 chr2:85811685-85811700 chr2:85811685-85811699
38	MAX	chr2:85810386-85812771	HepG2	liver:	n/a	n/a
39	BATF	chr2:85811215-85811484	GM12878	blood:	n/a	n/a
40	HNF4A	chr2:85811178-85811968	HepG2	liver:	n/a	chr2:85811685-85811699 chr2:85811685-85811700 chr2:85811685-85811700 chr2:85811686-85811698 chr2:85811685-85811700 chr2:85811686-85811698 chr2:85811683-85811701 chr2:85811686-85811694 chr2:85811684-85811699 chr2:85811685-85811700 chr2:85811685-85811699
41	TBP	chr2:85810846-85812499	HepG2	liver:	n/a	n/a
42	HNF4G	chr2:85811153-85812028	HepG2	liver:	n/a	chr2:85811685-85811699 chr2:85811685-85811700 chr2:85811685-85811700 chr2:85811686-85811698 chr2:85811685-85811700 chr2:85811686-85811698 chr2:85811683-85811701 chr2:85811686-85811694 chr2:85811685-85811700 chr2:85811685-85811699
43	RFX5	chr2:85810959-85811251	HepG2	liver:	n/a	n/a
44	EP300	chr2:85810913-85812662	HepG2	liver:	n/a	chr2:85812248-85812258 chr2:85811597-85811606 chr2:85812586-85812595
45	MXI1	chr2:85810818-85812703	HepG2	liver:	n/a	n/a
46	HEY1	chr2:85810714-85812895	HepG2	liver:	n/a	n/a
47	PML	chr2:85810981-85811893	GM12878	blood:	n/a	chr2:85811574-85811582
48	CEBPB	chr2:85810887-85811293	HepG2	liver:	n/a	chr2:85811094-85811105
49	MBD4	chr2:85810667-85813225	HepG2	liver:	n/a	n/a
50	POLR2A	chr2:85811222-85811901	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:85764476..85768967-chr2:85811222..85814196,4	MCF-7	breast:
2	chr2:85635981..85638120-chr2:85810202..85812459,2	MCF-7	breast:
3	chr2:85764082..85769632-chr2:85809376..85814783,9	K562	blood:
4	chr11:62609099..62611153-chr2:85810884..85812962,2	K562	blood:
5	chr2:85764767..85768368-chr2:85809376..85813309,5	K562	blood:
6	chr2:85764932..85768576-chr2:85809550..85811376,5	MCF-7	breast:
7	chr2:85788681..85792834-chr2:85809475..85813834,4	MCF-7	breast:

Variant related genes	Relation type
VAMP5	TF binding region
ENSG00000168906	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000042493	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10206961	0.82[YRI][hapmap]
rs1254897	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1254898	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62164837	0.84[AFR][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1254901	GGCX	cis	parietal	SCAN
rs1254901	RNF103	cis	parietal	SCAN
rs1254901	VAMP8	cis	lymphoblastoid	seeQTL
rs1254901	VAMP8	Cis_1M	lymphoblastoid	RTeQTL
rs1254901	GGCX	cis	cerebellum	SCAN
rs1254901	RETSAT	cis	cerebellum	SCAN
rs1254901	CD8A	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85806200-85811800	Weak transcription	A549	lung
2	chr2:85807000-85811400	Weak transcription	Small Intestine	intestine
3	chr2:85807600-85811600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:85807600-85812400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:85807800-85811800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:85807800-85812000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:85809400-85811800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr2:85809800-85811600	Weak transcription	HMEC	breast
9	chr2:85810000-85811600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:85810600-85811600	Enhancers	Spleen	Spleen
11	chr2:85810800-85811400	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr2:85810800-85811400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr2:85810800-85811400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr2:85810800-85811400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:85810800-85811400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr2:85810800-85811400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr2:85810800-85811400	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr2:85810800-85811400	Flanking Active TSS	Brain Substantia Nigra	brain
19	chr2:85810800-85811400	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr2:85810800-85811400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr2:85810800-85811400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr2:85810800-85811400	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr2:85810800-85811400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr2:85810800-85811600	Enhancers	Placenta Amnion	Placenta Amnion
25	chr2:85810800-85811800	Active TSS	Osteobl	bone
26	chr2:85810800-85812000	Active TSS	Brain Anterior Caudate	brain
27	chr2:85810800-85812000	Genic enhancers	Hela-S3	cervix
28	chr2:85810800-85812000	Genic enhancers	K562	blood
29	chr2:85810800-85812200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
30	chr2:85810800-85813000	Flanking Active TSS	Dnd41	blood
31	chr2:85810800-85813200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:85811000-85811400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:85811000-85811400	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr2:85811000-85811400	Flanking Active TSS	Primary B cells from peripheral blood	blood
35	chr2:85811000-85811400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
36	chr2:85811000-85811400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:85811000-85811400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:85811000-85811400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:85811000-85811400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr2:85811000-85811400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:85811000-85811400	Flanking Active TSS	Brain Angular Gyrus	brain
42	chr2:85811000-85811400	Flanking Active TSS	Brain Cingulate Gyrus	brain
43	chr2:85811000-85811400	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr2:85811000-85811400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr2:85811000-85811400	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
46	chr2:85811000-85811400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
47	chr2:85811000-85811400	Flanking Active TSS	Rectal Smooth Muscle	rectum
48	chr2:85811000-85811400	Flanking Active TSS	Right Atrium	heart
49	chr2:85811000-85811400	Flanking Active TSS	GM12878-XiMat	blood
50	chr2:85811000-85811400	Flanking Active TSS	HSMMtube	muscle

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