Variant report

Variant	rs2792434
Chromosome Location	chr7:150929476-150929477
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	HDAC2	chr7:150929280-150929784	K562	blood:	n/a	chr7:150929505-150929514
2	BACH1	chr7:150929146-150929630	H1-hESC	embryonic stem cell:	n/a	n/a
3	JUND	chr7:150929457-150929680	H1-hESC	embryonic stem cell:	n/a	n/a
4	PML	chr7:150928905-150930473	GM12878	blood:	n/a	chr7:150930373-150930382
5	SIN3AK20	chr7:150929312-150929908	H1-hESC	embryonic stem cell:	n/a	n/a
6	ETS1	chr7:150929306-150929765	GM12878	blood:	n/a	chr7:150929718-150929729 chr7:150929506-150929517 chr7:150929563-150929574
7	POLR2A	chr7:150929222-150930534	GM18526	blood:	n/a	n/a
8	MAX	chr7:150929293-150929504	HepG2	liver:	n/a	chr7:150929302-150929312
9	ZNF143	chr7:150929329-150929744	GM12878	blood:	n/a	chr7:150929508-150929518 chr7:150929720-150929738
10	SP1	chr7:150929290-150929746	GM12878	blood:	n/a	chr7:150929711-150929723 chr7:150929718-150929727 chr7:150929717-150929726 chr7:150929716-150929728 chr7:150929717-150929726 chr7:150929716-150929728 chr7:150929717-150929727 chr7:150929717-150929727 chr7:150929706-150929716 chr7:150929717-150929731
11	POLR2A	chr7:150929273-150929744	GM12891	blood:	n/a	n/a
12	TAF1	chr7:150929263-150929749	HepG2	liver:	n/a	n/a
13	POLR2A	chr7:150929219-150930609	GM12892	blood:	n/a	n/a
14	STAT5A	chr7:150929184-150930640	GM12878	blood:	n/a	chr7:150929713-150929725
15	POLR2A	chr7:150929274-150929814	K562	blood:	n/a	n/a
16	JUND	chr7:150929249-150929836	A549	lung:	n/a	chr7:150929418-150929427
17	MAX	chr7:150929174-150930098	ECC-1	luminal epithelium:	n/a	chr7:150929719-150929729 chr7:150929302-150929312
18	YY1	chr7:150929332-150929601	GM12891	blood:	n/a	n/a
19	TAF1	chr7:150929414-150929704	GM12878	blood:	n/a	n/a
20	POLR2A	chr7:150929161-150930929	U87	brain:	n/a	n/a
21	PAX5	chr7:150929215-150929807	GM12878	blood:	n/a	n/a
22	TAF1	chr7:150929363-150929682	GM12891	blood:	n/a	n/a
23	ELF1	chr7:150929258-150929820	SK-N-SH	brain:	n/a	chr7:150929710-150929719 chr7:150929566-150929577 chr7:150929615-150929627 chr7:150929771-150929783
24	RCOR1	chr7:150929145-150929840	HepG2	liver:	n/a	n/a
25	TAF1	chr7:150929287-150929768	GM12892	blood:	n/a	n/a
26	ELK4	chr7:150929202-150929737	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr7:150929227-150930698	GM18505	blood:	n/a	n/a
28	POLR2A	chr7:150929107-150930873	GM12878	blood:	n/a	n/a
29	ZBTB33	chr7:150929233-150929712	A549	lung:	n/a	n/a
30	POLR2A	chr7:150929304-150929749	A549	lung:	n/a	n/a
31	SPI1	chr7:150929404-150929740	GM12878	blood:	n/a	chr7:150929568-150929577 chr7:150929569-150929576 chr7:150929653-150929666 chr7:150929646-150929659 chr7:150929718-150929731
32	GABPA	chr7:150929024-150929902	A549	lung:	n/a	chr7:150929718-150929727 chr7:150929508-150929517
33	SRF	chr7:150929304-150929786	ECC-1	luminal epithelium:	n/a	chr7:150929719-150929729
34	POLR2A	chr7:150929223-150930627	Hela-S3	cervix:	n/a	n/a
35	RCOR1	chr7:150929040-150929855	GM12878	blood:	n/a	n/a
36	ELF1	chr7:150929365-150929726	HepG2	liver:	n/a	chr7:150929710-150929719 chr7:150929566-150929577 chr7:150929615-150929627
37	POLR2A	chr7:150929364-150929744	H1-hESC	embryonic stem cell:	n/a	n/a
38	SP2	chr7:150929330-150929733	K562	blood:	n/a	n/a
39	SP1	chr7:150929143-150929786	A549	lung:	n/a	chr7:150929711-150929723 chr7:150929718-150929727 chr7:150929717-150929726 chr7:150929716-150929728 chr7:150929717-150929726 chr7:150929716-150929728 chr7:150929717-150929727 chr7:150929717-150929727 chr7:150929706-150929716 chr7:150929717-150929731
40	FOXM1	chr7:150929024-150929866	GM12878	blood:	n/a	n/a
41	PBX3	chr7:150929387-150929650	GM12878	blood:	n/a	chr7:150929551-150929560
42	HEY1	chr7:150929364-150929777	HepG2	liver:	n/a	chr7:150929606-150929621 chr7:150929603-150929618
43	POLR2A	chr7:150929072-150930789	PBDE	blood:	n/a	n/a
44	YY1	chr7:150929111-150929722	SK-N-SH_RA	brain:	n/a	chr7:150929599-150929613 chr7:150929710-150929719
45	EBF1	chr7:150929098-150929702	GM12878	blood:	n/a	n/a
46	POLR2A	chr7:150929075-150930662	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr7:150929325-150929745	HepG2	liver:	n/a	n/a
48	MXI1	chr7:150929338-150929720	HepG2	liver:	n/a	chr7:150929532-150929547
49	POLR2A	chr7:150929234-150929772	SK-N-MC	brain:	n/a	n/a
50	BCL3	chr7:150929081-150929786	A549	lung:	n/a	chr7:150929612-150929621 chr7:150929436-150929449 chr7:150929712-150929721 chr7:150929599-150929612

No.	Distal block	Cell Line	Cell type
1	chr7:150928662..150932139-chr7:150946772..150952684,6	MCF-7	breast:
2	chr7:150904819..150907851-chr7:150927889..150929495,3	MCF-7	breast:
3	chr7:150811889..150814867-chr7:150929281..150931083,2	MCF-7	breast:
4	chr7:150862132..150865299-chr7:150928833..150931121,3	MCF-7	breast:
5	chr17:44269917..44270899-chr7:150928967..150929692,2	NB4	blood:
6	chr7:150928143..150930111-chr7:150944656..150946614,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ABCF2-2	chr7:150928545-150930322	NONHSAT124201

Variant related genes	Relation type
CHPF2	TF binding region
ENSG00000082014	Chromatin interaction
ENSG00000133612	Chromatin interaction
ENSG00000164900	Chromatin interaction
ENSG00000243018	Chromatin interaction
ENSG00000120071	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1870238	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242141	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2256864	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2414	0.84[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2429248	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2446065	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2487152	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2487154	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2487155	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2608288	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2608291	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs2608292	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2608293	0.80[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2792435	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2792436	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3800792	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3800793	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4725398	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4726009	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4726010	0.88[ASN][1000 genomes]
rs6464134	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6949587	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs758249	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]
rs897917	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs921987	0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv435860	chr7:150923672-150930735	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2792434	ABCF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150928600-150929600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr7:150928800-150930400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:150928800-150930400	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr7:150928800-150930600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr7:150928800-150930600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr7:150928800-150930600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr7:150928800-150931000	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr7:150929000-150929600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr7:150929000-150929600	Flanking Active TSS	HUVEC	blood vessel
10	chr7:150929000-150930000	Active TSS	Colonic Mucosa	Colon
11	chr7:150929000-150930400	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr7:150929000-150930400	Active TSS	Left Ventricle	heart
13	chr7:150929000-150930600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr7:150929000-150930600	Active TSS	H9 Cell Line	embryonic stem cell
15	chr7:150929000-150930600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr7:150929000-150930600	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr7:150929000-150930600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr7:150929000-150930600	Active TSS	Aorta	Aorta
19	chr7:150929000-150930800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr7:150929000-150930800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
21	chr7:150929000-150931000	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr7:150929000-150931000	Active TSS	Psoas Muscle	Psoas
23	chr7:150929000-150931200	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr7:150929000-150931600	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr7:150929200-150929800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr7:150929200-150929800	Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr7:150929200-150929800	Transcr. at gene 5' and 3'	Right Atrium	heart
28	chr7:150929200-150930000	Active TSS	Brain Cingulate Gyrus	brain
29	chr7:150929200-150930000	Active TSS	Brain Hippocampus Middle	brain
30	chr7:150929200-150930000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr7:150929200-150930000	Active TSS	Fetal Brain Female	brain
32	chr7:150929200-150930000	Active TSS	Fetal Lung	lung
33	chr7:150929200-150930200	Active TSS	H1 Cell Line	embryonic stem cell
34	chr7:150929200-150930200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr7:150929200-150930200	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr7:150929200-150930200	Active TSS	Brain Substantia Nigra	brain
37	chr7:150929200-150930200	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr7:150929200-150930400	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr7:150929200-150930400	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr7:150929200-150930400	Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr7:150929200-150930400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr7:150929200-150930400	Active TSS	Brain Angular Gyrus	brain
43	chr7:150929200-150930400	Active TSS	Fetal Intestine Large	intestine
44	chr7:150929200-150930400	Active TSS	Gastric	stomach
45	chr7:150929200-150930400	Active TSS	Ovary	ovary
46	chr7:150929200-150930400	Active TSS	Placenta Amnion	Placenta Amnion
47	chr7:150929200-150930400	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr7:150929200-150930400	Active TSS	Small Intestine	intestine
49	chr7:150929200-150930400	Active TSS	A549	lung
50	chr7:150929200-150930600	Active TSS	Fetal Kidney	kidney

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