Variant report

Variant	rs2968789
Chromosome Location	chr2:55278632-55278633
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	TCF12	chr2:55277108-55278970	SK-N-SH	brain:	n/a	chr2:55277949-55277956 chr2:55278509-55278518
2	JUND	chr2:55278209-55278693	HepG2	liver:	n/a	chr2:55278401-55278411 chr2:55278400-55278412 chr2:55278401-55278411 chr2:55278398-55278409 chr2:55278402-55278411 chr2:55278401-55278411 chr2:55278401-55278411 chr2:55278400-55278411
3	FOSL1	chr2:55278181-55278739	K562	blood:	n/a	chr2:55278401-55278411 chr2:55278400-55278412 chr2:55278401-55278411 chr2:55278398-55278409 chr2:55278402-55278411 chr2:55278400-55278411 chr2:55278401-55278411 chr2:55278401-55278411
4	MAFK	chr2:55278287-55278822	HepG2	liver:	n/a	chr2:55278509-55278518
5	RXRA	chr2:55278157-55278728	SK-N-SH	brain:	n/a	n/a
6	MAX	chr2:55277384-55278893	A549	lung:	n/a	chr2:55278420-55278430
7	TEAD4	chr2:55277123-55278992	K562	blood:	n/a	n/a
8	GABPA	chr2:55277388-55278643	MCF-7	breast:	n/a	n/a
9	BCL3	chr2:55277282-55278900	A549	lung:	n/a	chr2:55277604-55277613 chr2:55277645-55277654 chr2:55278055-55278064
10	POLR2A	chr2:55275958-55278821	HUVEC	blood vessel:	n/a	n/a
11	UBTF	chr2:55274752-55278735	K562	blood:	n/a	n/a
12	SMARCC1	chr2:55277068-55278785	Hela-S3	cervix:	n/a	chr2:55278402-55278411 chr2:55277702-55277711
13	POLR2A	chr2:55277116-55278826	PBDE	blood:	n/a	n/a
14	POLR2A	chr2:55276933-55278685	K562	blood:	n/a	n/a
15	NR2F2	chr2:55277170-55278978	K562	blood:	n/a	n/a
16	POLR2A	chr2:55275602-55278945	HCT-116	colon:	n/a	n/a
17	STAT3	chr2:55278274-55278791	MCF10A-Er-Src	breast:	n/a	chr2:55278443-55278450
18	ATF3	chr2:55278147-55278717	K562	blood:	n/a	n/a
19	SIN3A	chr2:55275650-55278654	H1-hESC	embryonic stem cell:	n/a	chr2:55276189-55276200
20	RCOR1	chr2:55275614-55278876	Hela-S3	cervix:	n/a	n/a
21	BRCA1	chr2:55277481-55279097	Hela-S3	cervix:	n/a	chr2:55277795-55277802
22	POLR2A	chr2:55277242-55278783	HUVEC	blood vessel:	n/a	n/a
23	JUN	chr2:55278209-55278680	K562	blood:	n/a	chr2:55278401-55278411 chr2:55278400-55278412 chr2:55278401-55278411 chr2:55278398-55278409 chr2:55278402-55278411 chr2:55278401-55278411 chr2:55278401-55278411
24	JUND	chr2:55278109-55278795	A549	lung:	n/a	chr2:55278401-55278411 chr2:55278400-55278412 chr2:55278401-55278411 chr2:55278398-55278409 chr2:55278402-55278411 chr2:55278401-55278411 chr2:55278401-55278411 chr2:55278400-55278411
25	POLR2A	chr2:55277032-55278781	PANC-1	pancreas:	n/a	n/a
26	SIN3AK20	chr2:55277897-55278908	A549	lung:	n/a	n/a
27	FOSL2	chr2:55278094-55278782	MCF-7	breast:	n/a	chr2:55278401-55278411 chr2:55278400-55278412 chr2:55278401-55278411 chr2:55278398-55278409 chr2:55278401-55278412 chr2:55278402-55278411 chr2:55278401-55278411 chr2:55278401-55278411
28	MTA3	chr2:55277082-55278821	GM12878	blood:	n/a	n/a
29	MAFK	chr2:55278216-55278984	Hela-S3	cervix:	n/a	chr2:55278509-55278518
30	MEF2A	chr2:55278137-55278869	SK-N-SH	brain:	n/a	chr2:55278139-55278154
31	TEAD4	chr2:55278217-55278923	ECC-1	luminal epithelium:	n/a	n/a
32	POLR2A	chr2:55275829-55278945	SK-N-MC	brain:	n/a	n/a
33	MYBL2	chr2:55277192-55278721	HepG2	liver:	n/a	n/a
34	FOSL2	chr2:55278186-55278655	HepG2	liver:	n/a	chr2:55278401-55278411 chr2:55278400-55278412 chr2:55278401-55278411 chr2:55278398-55278409 chr2:55278401-55278412 chr2:55278402-55278411 chr2:55278401-55278411 chr2:55278401-55278411
35	TCF12	chr2:55277846-55278828	A549	lung:	n/a	chr2:55277949-55277956 chr2:55278509-55278518
36	TCF12	chr2:55275501-55278974	A549	lung:	n/a	chr2:55277949-55277956 chr2:55275946-55275954 chr2:55278509-55278518
37	BACH1	chr2:55277603-55278725	H1-hESC	embryonic stem cell:	n/a	chr2:55277699-55277713
38	RXRA	chr2:55277975-55278933	SK-N-SH	brain:	n/a	chr2:55278024-55278044
39	MXI1	chr2:55275607-55278907	IMR90	lung:	n/a	n/a
40	MAX	chr2:55277085-55278950	A549	lung:	n/a	chr2:55278420-55278430
41	TEAD4	chr2:55277956-55278925	SK-N-SH	brain:	n/a	n/a
42	TAF1	chr2:55278217-55278717	SK-N-SH	brain:	n/a	n/a
43	JUN	chr2:55275513-55278923	K562	blood:	n/a	chr2:55278401-55278411 chr2:55278400-55278412 chr2:55278401-55278411 chr2:55278398-55278409 chr2:55278402-55278411 chr2:55278401-55278411 chr2:55277702-55277711 chr2:55278401-55278411
44	JUND	chr2:55277096-55279068	SK-N-SH	brain:	n/a	chr2:55278401-55278411 chr2:55278400-55278412 chr2:55278401-55278411 chr2:55278398-55278409 chr2:55278402-55278411 chr2:55278401-55278411 chr2:55277700-55277711 chr2:55277702-55277711 chr2:55278401-55278411 chr2:55278400-55278411
45	POLR2A	chr2:55275591-55278852	K562	blood:	n/a	n/a
46	PBX3	chr2:55277251-55278860	SK-N-SH	brain:	n/a	chr2:55277751-55277760 chr2:55277777-55277797
47	POLR2A	chr2:55275124-55278891	Hela-S3	cervix:	n/a	n/a
48	MAFF	chr2:55278342-55278700	HepG2	liver:	n/a	n/a
49	ZC3H11A	chr2:55277995-55278784	K562	blood:	n/a	n/a
50	POLR2A	chr2:55278195-55278690	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55276798..55279791-chr2:55841794..55843892,2	K562	blood:
2	chr2:55278226..55280278-chr2:55389625..55391199,2	MCF-7	breast:
3	chr2:55273237..55280299-chr2:55335301..55344768,18	K562	blood:
4	chr2:55275304..55279887-chr2:55458370..55461390,5	K562	blood:
5	chr2:55278214..55278967-chr2:88926117..88926888,2	Hela-S3	cervix:
6	chr2:55278333..55279964-chr2:55343174..55345064,2	MCF-7	breast:
7	chr2:55278606..55281085-chr2:55289009..55290511,2	K562	blood:
8	chr2:55276121..55279274-chr2:55457448..55460901,6	K562	blood:
9	chr2:55273237..55279836-chr2:55336432..55344363,17	K562	blood:
10	chr2:55278300..55281080-chr2:55325086..55327233,3	K562	blood:
11	chr2:55276251..55278794-chr2:55450594..55452106,2	MCF-7	breast:

Variant related genes	Relation type
RTN4	TF binding region
ENSG00000138041	Chromatin interaction
ENSG00000162994	Chromatin interaction
ENSG00000115310	Chromatin interaction
ENSG00000227799	Chromatin interaction
ENSG00000266376	Chromatin interaction
ENSG00000143947	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10179594	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10196667	0.82[CEU][hapmap];0.82[MEX][hapmap]
rs10205017	0.88[EUR][1000 genomes]
rs10746530	0.82[CEU][hapmap]
rs11125551	0.82[CEU][hapmap]
rs12989576	0.82[CEU][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes]
rs13002841	0.82[CEU][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];0.87[EUR][1000 genomes]
rs13023202	0.89[EUR][1000 genomes]
rs17417648	0.82[CHB][hapmap]
rs2580763	0.93[JPT][hapmap];0.85[EUR][1000 genomes]
rs2580766	0.82[CEU][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes]
rs2588520	0.82[CEU][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes]
rs2919125	0.82[CEU][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes]
rs2920839	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920861	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2920863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2920881	1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2920883	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2920884	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2920889	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2920890	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2920897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2920898	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs2968792	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2968812	1.00[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap]
rs2968813	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2968814	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2968823	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2968824	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2968826	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2968829	1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs2968831	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972065	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2972066	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2972067	0.81[ASN][1000 genomes]
rs2972069	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2972073	0.81[ASN][1000 genomes]
rs2972076	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3099068	0.81[ASN][1000 genomes]
rs6545462	0.82[CEU][hapmap]
rs72912591	0.92[AFR][1000 genomes]
rs7559248	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2968789	VPS37B	trans	lymphoblastoid	seeQTL
rs2968789	RTN4	cis	Thyroid	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55272400-55279600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr2:55273400-55279800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr2:55273800-55279000	Active TSS	Psoas Muscle	Psoas
4	chr2:55273800-55279200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:55274200-55279000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:55274200-55279200	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr2:55274200-55279600	Active TSS	HMEC	breast
8	chr2:55274400-55278800	Active TSS	Fetal Brain Male	brain
9	chr2:55274600-55278800	Active TSS	Aorta	Aorta
10	chr2:55274600-55278800	Active TSS	Fetal Muscle Trunk	muscle
11	chr2:55274600-55279200	Active TSS	NHEK	skin
12	chr2:55274800-55278800	Active TSS	Ovary	ovary
13	chr2:55274800-55279000	Active TSS	H9 Cell Line	embryonic stem cell
14	chr2:55274800-55279000	Active TSS	Right Ventricle	heart
15	chr2:55275000-55278800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:55275000-55278800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:55275000-55279400	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr2:55275000-55279400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:55275200-55278800	Active TSS	Left Ventricle	heart
20	chr2:55275200-55279200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:55275400-55278800	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr2:55275400-55279000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:55275400-55279600	Active TSS	A549	lung
24	chr2:55275600-55278800	Active TSS	HSMM	muscle
25	chr2:55275800-55279200	Active TSS	Thymus	Thymus
26	chr2:55275800-55280000	Active TSS	NHLF	lung
27	chr2:55276200-55279200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:55277400-55279000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:55277400-55279200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:55277800-55279000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:55277800-55279400	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr2:55277800-55279800	Active TSS	Right Atrium	heart
33	chr2:55278000-55278800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
34	chr2:55278000-55278800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr2:55278000-55278800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr2:55278000-55279000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr2:55278000-55279000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr2:55278000-55279000	Flanking Active TSS	Osteobl	bone
39	chr2:55278000-55279400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr2:55278000-55279400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr2:55278000-55279600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr2:55278000-55280000	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr2:55278000-55280000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:55278000-55280200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:55278200-55278800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr2:55278200-55278800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr2:55278200-55278800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr2:55278200-55278800	Flanking Active TSS	Fetal Intestine Large	intestine
49	chr2:55278200-55278800	Flanking Active TSS	Fetal Thymus	thymus
50	chr2:55278200-55278800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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