Variant report

Variant	rs7589600
Chromosome Location	chr2:189159092-189159093
allele	G/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	RCOR1	chr2:189158707-189159281	K562	blood:	n/a	n/a
2	TBL1XR1	chr2:189158638-189159161	K562	blood:	n/a	n/a
3	POLR2A	chr2:189155830-189159188	H1-hESC	embryonic stem cell:	n/a	n/a
4	EP300	chr2:189158692-189159167	SK-N-SH_RA	brain:	n/a	n/a
5	FOS	chr2:189159042-189159531	MCF10A-Er-Src	breast:	n/a	n/a
6	CHD1	chr2:189156501-189161129	H1-hESC	embryonic stem cell:	n/a	n/a
7	GATA3	chr2:189158135-189159361	SK-N-SH	brain:	n/a	chr2:189158773-189158783 chr2:189158225-189158238 chr2:189158770-189158786 chr2:189158774-189158783
8	TCF7L2	chr2:189157273-189159132	HEK293	kidney:	n/a	chr2:189158847-189158857
9	SMC3	chr2:189155238-189159444	SK-N-SH	brain:	n/a	chr2:189157006-189157013
10	GATA3	chr2:189158163-189159250	SK-N-SH	brain:	n/a	chr2:189158773-189158783 chr2:189158225-189158238 chr2:189158770-189158786 chr2:189158774-189158783
11	RAD21	chr2:189155121-189159652	SK-N-SH	brain:	n/a	chr2:189157053-189157062 chr2:189157634-189157648
12	POLR2A	chr2:189156081-189159271	K562	blood:	n/a	n/a
13	TCF7L2	chr2:189158184-189159471	PANC-1	pancreas:	n/a	chr2:189158847-189158857
14	MAZ	chr2:189158395-189159142	K562	blood:	n/a	n/a
15	MXI1	chr2:189155279-189161412	SK-N-SH	brain:	n/a	n/a
16	SIN3A	chr2:189155875-189159442	H1-hESC	embryonic stem cell:	n/a	chr2:189156997-189157005
17	MXI1	chr2:189155585-189159113	IMR90	lung:	n/a	n/a
18	YY1	chr2:189158665-189159148	SK-N-SH_RA	brain:	n/a	n/a
19	POLR2A	chr2:189155767-189159411	SK-N-SH	brain:	n/a	n/a
20	EP300	chr2:189158238-189159170	K562	blood:	n/a	chr2:189158507-189158521
21	EP300	chr2:189158663-189159167	SK-N-SH_RA	brain:	n/a	n/a
22	TCF12	chr2:189155774-189159211	A549	lung:	n/a	chr2:189156082-189156089
23	TAF7	chr2:189155840-189159451	H1-hESC	embryonic stem cell:	n/a	n/a
24	GATA2	chr2:189158288-189159131	SH-SY5Y	brain:	n/a	chr2:189158773-189158783 chr2:189158770-189158786 chr2:189158774-189158783
25	JUND	chr2:189157990-189159641	K562	blood:	n/a	chr2:189159582-189159592 chr2:189159582-189159592 chr2:189158890-189158899 chr2:189159582-189159592 chr2:189159582-189159592
26	BHLHE40	chr2:189155783-189159120	K562	blood:	n/a	n/a
27	NFIC	chr2:189156237-189159350	SK-N-SH	brain:	n/a	chr2:189158527-189158543 chr2:189158526-189158543 chr2:189158525-189158542
28	JUND	chr2:189158700-189159207	H1-hESC	embryonic stem cell:	n/a	chr2:189158890-189158899
29	CCNT2	chr2:189158675-189159174	K562	blood:	n/a	n/a
30	POLR2A	chr2:189155963-189159240	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr2:189155173-189159469	H1-hESC	embryonic stem cell:	n/a	n/a
32	CEBPB	chr2:189158629-189159160	K562	blood:	n/a	chr2:189158643-189158656
33	KAP1	chr2:189155749-189159564	HEK293	kidney:	n/a	chr2:189158519-189158527 chr2:189156384-189156392
34	KAP1	chr2:189155854-189159403	U2OS	brain:	n/a	chr2:189158519-189158527 chr2:189156384-189156392

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:189148121..189153367-chr2:189154784..189162424,9	K562	blood:

Variant related genes	Relation type
MIR561	TF binding region
ENSG00000231689	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10153666	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10153862	1.00[AMR][1000 genomes]
rs10171583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10174521	1.00[AMR][1000 genomes]
rs10184797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10185493	0.88[AFR][1000 genomes]
rs10190081	0.93[AFR][1000 genomes]
rs10190630	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10192679	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10197598	0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs10198965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10199401	1.00[AFR][1000 genomes]
rs10207510	1.00[AMR][1000 genomes]
rs10211425	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10211482	1.00[AMR][1000 genomes]
rs10439261	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13386579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13390367	1.00[AMR][1000 genomes]
rs13391799	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13392080	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13393442	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs13399616	0.83[YRI][hapmap]
rs13399903	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13401242	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs13401321	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13401975	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13402240	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13403508	1.00[MEX][hapmap];0.94[MKK][hapmap]
rs13403672	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13404901	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13411351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13414813	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13418323	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13423468	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13424443	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28528331	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59080597	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6434282	0.83[YRI][hapmap]
rs6434283	0.83[YRI][hapmap]
rs6434287	1.00[AMR][1000 genomes]
rs6705869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6710795	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs6742748	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6744742	0.83[YRI][hapmap]
rs6748075	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6755644	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs6759147	0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs9288154	0.91[AFR][1000 genomes]
rs9288156	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010394	chr2:188994398-189284092	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
2	nsv998395	chr2:189018246-189284092	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7589600	FERMT2	trans	lymphoblastoid	seeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189155200-189161800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr2:189155400-189160800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:189155400-189161000	Active TSS	Aorta	Aorta
4	chr2:189155400-189161200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:189155400-189161200	Active TSS	K562	blood
6	chr2:189155400-189161600	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr2:189155600-189161200	Active TSS	H9 Cell Line	embryonic stem cell
8	chr2:189155600-189161600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:189155600-189161800	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr2:189155800-189159200	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr2:189155800-189159200	Active TSS	Ovary	ovary
12	chr2:189155800-189159200	Active TSS	Psoas Muscle	Psoas
13	chr2:189155800-189159400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:189155800-189159400	Active TSS	Fetal Intestine Small	intestine
15	chr2:189155800-189159400	Active TSS	Right Atrium	heart
16	chr2:189155800-189159800	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr2:189155800-189160000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:189155800-189160200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr2:189155800-189160200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:189155800-189160200	Active TSS	Fetal Intestine Large	intestine
21	chr2:189155800-189161200	Active TSS	Placenta	Placenta
22	chr2:189155800-189161200	Active TSS	A549	lung
23	chr2:189155800-189161400	Active TSS	H1 Cell Line	embryonic stem cell
24	chr2:189156000-189159200	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr2:189156000-189159200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:189156000-189159200	Active TSS	Colon Smooth Muscle	Colon
27	chr2:189156000-189159600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr2:189156000-189159600	Active TSS	Stomach Smooth Muscle	stomach
29	chr2:189156000-189159800	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr2:189156000-189160000	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr2:189156000-189160000	Active TSS	Brain Angular Gyrus	brain
32	chr2:189156000-189161000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:189156000-189161200	Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr2:189156000-189161600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr2:189156200-189159400	Active TSS	Colonic Mucosa	Colon
36	chr2:189156200-189160800	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr2:189156400-189159400	Active TSS	Duodenum Mucosa	Duodenum
38	chr2:189156400-189160400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:189156600-189159400	Active TSS	Rectal Mucosa Donor 31	rectum
40	chr2:189156800-189159200	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr2:189157400-189160000	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr2:189157600-189159400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr2:189157600-189159400	Active TSS	Brain Germinal Matrix	brain
44	chr2:189157800-189159200	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
45	chr2:189157800-189159800	Flanking Active TSS	NH-A	brain
46	chr2:189158000-189159600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:189158000-189163600	Weak transcription	Lung	lung
48	chr2:189158200-189159200	Enhancers	Brain Substantia Nigra	brain
49	chr2:189158200-189159200	Flanking Active TSS	Osteobl	bone
50	chr2:189158200-189159400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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