Variant report

Variant	rs758249
Chromosome Location	chr7:150941238-150941239
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	CTCF	chr7:150941224-150941839	K562	blood:	n/a	chr7:150941560-150941581
2	CTCF	chr7:150941199-150941683	GM12892	blood:	n/a	chr7:150941560-150941581
3	RAD21	chr7:150941212-150941706	H1-hESC	embryonic stem cell:	n/a	chr7:150941591-150941603 chr7:150941563-150941582
4	CTCF	chr7:150941160-150941310	WERI-Rb-1	eye:	n/a	n/a
5	MTA3	chr7:150940959-150941740	GM12878	blood:	n/a	n/a
6	SMC3	chr7:150940796-150943624	SK-N-SH	brain:	n/a	chr7:150941980-150941987 chr7:150941567-150941581 chr7:150941940-150941947
7	CTCF	chr7:150940291-150943350	SK-N-SH	brain:	n/a	chr7:150941938-150941951 chr7:150940479-150940497 chr7:150941560-150941581 chr7:150941941-150941954 chr7:150940585-150940598 chr7:150941920-150941929 chr7:150941977-150941986
8	POLR2A	chr7:150940719-150941426	U87	brain:	n/a	n/a
9	CTCF	chr7:150941211-150941404	GM19239	blood:	n/a	n/a
10	CTCF	chr7:150941231-150941697	K562	blood:	n/a	chr7:150941560-150941581
11	POLR2A	chr7:150935782-150941408	U87	brain:	n/a	n/a
12	POLR2A	chr7:150941077-150942207	IMR90	lung:	n/a	n/a
13	POLR2A	chr7:150932457-150941238	U87	brain:	n/a	n/a
14	POLR2A	chr7:150940769-150941426	U87	brain:	n/a	n/a
15	CTCF	chr7:150941169-150941689	GM19238	blood:	n/a	chr7:150941560-150941581
16	POLR2A	chr7:150941141-150941241	Hela-S3	cervix:	n/a	n/a
17	MAZ	chr7:150941113-150942163	IMR90	lung:	n/a	n/a
18	POLR2A	chr7:150941224-150941391	MCF-7	breast:	n/a	n/a
19	CTCF	chr7:150941215-150941668	GM12891	blood:	n/a	chr7:150941560-150941581
20	ZNF263	chr7:150940920-150941537	HEK293-T-REx	kidney:	n/a	chr7:150941123-150941144
21	RAD21	chr7:150940770-150943041	SK-N-SH	brain:	n/a	chr7:150941937-150941950 chr7:150941591-150941603 chr7:150941563-150941582 chr7:150941940-150941954

No.	Distal block	Cell Line	Cell type
1	chr7:150869379..150870234-chr7:150941055..150942048,8	MCF-7	breast:
2	chr7:150888388..150889316-chr7:150941010..150942053,3	K562	blood:
3	chr7:150923495..150927436-chr7:150940006..150942925,4	MCF-7	breast:
4	chr7:150901645..150902197-chr7:150940945..150941682,2	K562	blood:
5	chr7:150869400..150870347-chr7:150941097..150942121,7	K562	blood:
6	chr7:150938571..150942838-chr7:150950941..150954111,4	MCF-7	breast:
7	chr7:150865018..150866330-chr7:150941109..150942155,6	K562	blood:
8	chr7:150820602..150821298-chr7:150941184..150941993,2	MCF-7	breast:
9	chr7:150819780..150822617-chr7:150940406..150943194,3	MCF-7	breast:

Variant related genes	Relation type
SMARCD3	TF binding region
ENSG00000082014	Chromatin interaction
ENSG00000033050	Chromatin interaction
ENSG00000133612	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1870238	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242141	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2256864	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2414	0.90[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2429248	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2446065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2487152	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2487154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2487155	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2608288	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2608291	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs2608292	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2608293	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2792434	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2792435	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2792436	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2792444	0.82[EUR][1000 genomes]
rs3800792	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3800793	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4725398	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4726009	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4726010	0.92[ASN][1000 genomes]
rs6464134	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6949587	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs897917	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs921987	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821419	chr7:150593315-150974269	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	128 gene(s)	inside rSNPs	diseases
2	nsv889476	chr7:150729212-150951819	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	120 gene(s)	inside rSNPs	diseases
3	nsv609035	chr7:150896223-150955765	Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv889487	chr7:150922952-150988172	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
5	nsv889488	chr7:150926775-150955765	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs758249	ABCF2	Cis_1M	lymphoblastoid	RTeQTL
rs758249	GIMAP6	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150931000-150944600	Weak transcription	Fetal Kidney	kidney
2	chr7:150931600-150944400	Weak transcription	Hela-S3	cervix
3	chr7:150932800-150942000	Weak transcription	Psoas Muscle	Psoas
4	chr7:150936400-150942200	Weak transcription	HMEC	breast
5	chr7:150936800-150941800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr7:150938600-150941800	Weak transcription	NH-A	brain
7	chr7:150939200-150941600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr7:150939200-150941600	Weak transcription	A549	lung
9	chr7:150939200-150942000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr7:150939200-150942000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr7:150939400-150941800	Enhancers	Fetal Brain Male	brain
12	chr7:150939400-150941800	Enhancers	HepG2	liver
13	chr7:150939600-150941800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr7:150939600-150941800	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr7:150939600-150942000	Weak transcription	Aorta	Aorta
16	chr7:150939800-150941400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr7:150939800-150941600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr7:150939800-150941600	Genic enhancers	Fetal Muscle Leg	muscle
19	chr7:150939800-150941600	Weak transcription	Osteobl	bone
20	chr7:150939800-150941800	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr7:150940000-150941400	Flanking Active TSS	Dnd41	blood
22	chr7:150940000-150941800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr7:150940000-150941800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr7:150940000-150942200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:150940000-150942200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr7:150940000-150942400	Bivalent Enhancer	Stomach Mucosa	stomach
27	chr7:150940000-150942800	Enhancers	Spleen	Spleen
28	chr7:150940200-150941400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr7:150940200-150941400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr7:150940200-150941400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr7:150940200-150941400	Genic enhancers	NHLF	lung
32	chr7:150940200-150941600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr7:150940200-150941600	Enhancers	Esophagus	oesophagus
34	chr7:150940200-150941800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr7:150940200-150941800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr7:150940200-150941800	Enhancers	Colon Smooth Muscle	Colon
37	chr7:150940200-150942000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
38	chr7:150940200-150942000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
39	chr7:150940200-150942000	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr7:150940200-150942200	Enhancers	Brain Cingulate Gyrus	brain
41	chr7:150940200-150942200	Flanking Active TSS	Fetal Brain Female	brain
42	chr7:150940200-150942600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr7:150940200-150942600	Enhancers	Lung	lung
44	chr7:150940200-150943000	Enhancers	Adipose Nuclei	Adipose
45	chr7:150940200-150944800	Enhancers	Pancreas	Pancrea
46	chr7:150940200-150945400	Enhancers	K562	blood
47	chr7:150940400-150941600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr7:150940400-150941600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr7:150940400-150941800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr7:150940400-150942000	Enhancers	Skeletal Muscle Female	skeletal muscle

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