Variant report

Variant	rs12705089
Chromosome Location	chr7:100465355-100465356
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	STAT5A	chr7:100464385-100465358	GM12878	blood:	n/a	chr7:100464668-100464680
2	POLR2A	chr7:100464031-100465440	MCF10A-Er-Src	breast:	n/a	n/a
3	HCFC1	chr7:100462784-100465378	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr7:100464308-100465543	K562	blood:	n/a	n/a
5	MAX	chr7:100464460-100465441	ECC-1	luminal epithelium:	n/a	chr7:100465338-100465348 chr7:100464740-100464747 chr7:100464920-100464931 chr7:100464921-100464930 chr7:100464916-100464935 chr7:100464730-100464746 chr7:100464666-100464676 chr7:100464919-100464932 chr7:100464739-100464748 chr7:100464921-100464930
6	SPI1	chr7:100464658-100465445	HL-60	blood:	n/a	n/a
7	POLR2A	chr7:100463239-100465982	Hela-S3	cervix:	n/a	n/a
8	MAX	chr7:100462763-100466194	HCT-116	colon:	n/a	chr7:100465338-100465348 chr7:100464740-100464747 chr7:100464920-100464931 chr7:100464921-100464930 chr7:100464916-100464935 chr7:100464730-100464746 chr7:100464666-100464676 chr7:100464919-100464932 chr7:100464739-100464748 chr7:100464921-100464930
9	USF1	chr7:100464154-100465379	HCT-116	colon:	n/a	chr7:100464920-100464931
10	POLR2A	chr7:100465257-100466093	K562	blood:	n/a	n/a
11	TAF1	chr7:100464650-100465387	H1-hESC	embryonic stem cell:	n/a	n/a
12	ZBTB7A	chr7:100464518-100465633	ECC-1	luminal epithelium:	n/a	n/a
13	SIN3A	chr7:100464627-100466064	H1-hESC	embryonic stem cell:	n/a	chr7:100464920-100464929 chr7:100464922-100464931
14	TCF3	chr7:100464965-100465409	GM12878	blood:	n/a	n/a
15	POLR2A	chr7:100463591-100465407	Hela-S3	cervix:	n/a	n/a
16	CHD1	chr7:100464918-100465765	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr7:100464594-100465449	GM19099	blood:	n/a	n/a
18	POLR2A	chr7:100465113-100465429	GM12891	blood:	n/a	n/a
19	POLR2A	chr7:100464633-100465410	GM18526	blood:	n/a	n/a
20	POLR2A	chr7:100464647-100465977	GM12892	blood:	n/a	n/a
21	MAZ	chr7:100464585-100465452	GM12878	blood:	n/a	chr7:100465338-100465348 chr7:100464740-100464747 chr7:100464920-100464931 chr7:100464921-100464930 chr7:100464916-100464935 chr7:100464730-100464746 chr7:100464666-100464676 chr7:100464919-100464932 chr7:100464739-100464748 chr7:100464921-100464930
22	ELF1	chr7:100464568-100465632	GM12878	blood:	n/a	chr7:100465335-100465347 chr7:100464759-100464771
23	POLR2A	chr7:100464677-100465381	MCF-7	breast:	n/a	n/a
24	ATF2	chr7:100464631-100465361	GM12878	blood:	n/a	n/a
25	HEY1	chr7:100464581-100465466	K562	blood:	n/a	chr7:100464949-100464958 chr7:100464947-100464956
26	POLR2A	chr7:100463267-100465502	Hela-S3	cervix:	n/a	n/a
27	SMARCB1	chr7:100463207-100466210	Hela-S3	cervix:	n/a	n/a
28	MAX	chr7:100463896-100465517	MCF-7	breast:	n/a	chr7:100465338-100465348 chr7:100464740-100464747 chr7:100464920-100464931 chr7:100464921-100464930 chr7:100464916-100464935 chr7:100464730-100464746 chr7:100464666-100464676 chr7:100464919-100464932 chr7:100464739-100464748 chr7:100464921-100464930
29	POLR2A	chr7:100464459-100466327	K562	blood:	n/a	n/a
30	POLR2A	chr7:100463164-100466642	HL-60	blood:	n/a	n/a
31	JUND	chr7:100464522-100465397	K562	blood:	n/a	chr7:100464883-100464893 chr7:100464882-100464893 chr7:100464948-100464957
32	HEY1	chr7:100464573-100466263	K562	blood:	n/a	chr7:100464949-100464958 chr7:100464947-100464956
33	POLR2A	chr7:100463598-100465376	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr7:100464560-100465931	GM18505	blood:	n/a	n/a
35	POLR2A	chr7:100464568-100465523	GM12878	blood:	n/a	n/a
36	POLR2A	chr7:100464584-100465501	H1-hESC	embryonic stem cell:	n/a	n/a
37	RUNX3	chr7:100464566-100465362	GM12878	blood:	n/a	chr7:100464822-100464837
38	CHD1	chr7:100464240-100466322	IMR90	lung:	n/a	n/a
39	TAF7	chr7:100464971-100465359	H1-hESC	embryonic stem cell:	n/a	n/a
40	MAZ	chr7:100464254-100465542	IMR90	lung:	n/a	chr7:100465338-100465348 chr7:100464740-100464747 chr7:100464920-100464931 chr7:100464921-100464930 chr7:100464916-100464935 chr7:100464730-100464746 chr7:100464666-100464676 chr7:100464919-100464932 chr7:100464739-100464748 chr7:100464921-100464930
41	CTBP2	chr7:100464702-100465374	H1-hESC	embryonic stem cell:	n/a	n/a
42	FOSL2	chr7:100464329-100465427	MCF-7	breast:	n/a	chr7:100464883-100464893 chr7:100464882-100464893 chr7:100464948-100464957
43	EGR1	chr7:100465248-100465694	K562	blood:	n/a	n/a
44	TFAP2C	chr7:100463185-100465413	Hela-S3	cervix:	n/a	chr7:100463791-100463806
45	POLR2A	chr7:100465008-100465513	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr7:100464097-100466221	GM12878	blood:	n/a	n/a
47	REST	chr7:100464542-100465363	HL-60	blood:	n/a	n/a
48	HMGN3	chr7:100464597-100465375	K562	blood:	n/a	chr7:100464885-100464894 chr7:100464882-100464891
49	UBTF	chr7:100464687-100466303	K562	blood:	n/a	n/a
50	POLR2A	chr7:100464567-100465474	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:100448977..100453392-chr7:100463620..100466806,5	K562	blood:
2	chr19:10443947..10444570-chr7:100464956..100465471,2	NB4	blood:
3	chr7:100448636..100452358-chr7:100462094..100466806,6	K562	blood:
4	chr7:100270217..100272304-chr7:100463855..100466313,2	MCF-7	breast:
5	chr2:181845181..181847277-chr7:100464247..100466142,2	MCF-7	breast:
6	chr7:100449368..100450252-chr7:100464960..100465806,2	MCF-7	breast:
7	chr7:100423752..100426266-chr7:100463292..100466439,3	MCF-7	breast:
8	chr7:100025401..100028370-chr7:100464359..100466273,3	K562	blood:
9	chr7:100270953..100272830-chr7:100463570..100466328,2	K562	blood:
10	chr7:100450046..100452057-chr7:100463309..100465619,3	MCF-7	breast:
11	chr7:100033419..100035678-chr7:100463885..100466048,2	MCF-7	breast:
12	chr7:100208537..100210261-chr7:100463099..100465535,2	MCF-7	breast:

Variant related genes	Relation type
TRIP6	TF binding region
ENSG00000236305	Chromatin interaction
ENSG00000170035	Chromatin interaction
ENSG00000196411	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000161847	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000106330	Chromatin interaction
ENSG00000172354	Chromatin interaction
ENSG00000146828	Chromatin interaction
ENSG00000160813	Chromatin interaction
ENSG00000240211	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12666989	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12667888	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12705090	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12705091	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12705092	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12705095	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12705096	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13226502	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13226864	0.90[EUR][1000 genomes]
rs13244629	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13245899	0.85[EUR][1000 genomes]
rs17881696	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17883557	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17884589	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs314324	0.84[ASN][1000 genomes]
rs314370	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs314373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757868	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6706	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv1020837	chr7:100313122-100508635	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1832517	chr7:100355490-100749246	Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	esv2758125	chr7:100355490-100749246	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	esv2759547	chr7:100355490-100749246	Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	nsv464647	chr7:100374087-100497131	Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv607965	chr7:100374087-100497131	Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
8	nsv1032673	chr7:100382250-100606794	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
9	nsv888797	chr7:100386900-100482026	Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
10	nsv888798	chr7:100406144-100472826	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
11	nsv888799	chr7:100406144-100497131	Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh 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	89 gene(s)	inside rSNPs	diseases
12	nsv888801	chr7:100416250-100497131	Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
13	nsv464648	chr7:100422156-100518458	Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
14	nsv607966	chr7:100422156-100518458	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
15	nsv831073	chr7:100425659-100544888	Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12705089	ACHE	cis	Artery Tibial	GTEx
rs12705089	ACHE	cis	Artery Aorta	GTEx
rs12705089	ACHE	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100461800-100471400	Weak transcription	HepG2	liver
2	chr7:100463400-100465400	Flanking Active TSS	Brain Germinal Matrix	brain
3	chr7:100463400-100465800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
4	chr7:100463400-100465800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr7:100463600-100466000	Flanking Active TSS	Fetal Muscle Leg	muscle
6	chr7:100463600-100466400	Flanking Active TSS	Brain Hippocampus Middle	brain
7	chr7:100463600-100466400	Active TSS	Psoas Muscle	Psoas
8	chr7:100463600-100466600	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr7:100464000-100465400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
10	chr7:100464000-100465400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr7:100464000-100465400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
12	chr7:100464000-100465600	Flanking Active TSS	Primary B cells from peripheral blood	blood
13	chr7:100464000-100465600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
14	chr7:100464000-100466200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr7:100464000-100466400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr7:100464000-100466600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr7:100464000-100466600	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr7:100464200-100465400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr7:100464200-100465400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr7:100464200-100465400	Flanking Active TSS	HSMMtube	muscle
21	chr7:100464200-100465600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr7:100464200-100465800	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr7:100464200-100466200	Flanking Active TSS	Placenta	Placenta
24	chr7:100464200-100466200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
25	chr7:100464400-100465400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr7:100464400-100465400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr7:100464400-100466400	Flanking Active TSS	Fetal Thymus	thymus
28	chr7:100464400-100466600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr7:100464600-100465400	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr7:100464600-100465400	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
31	chr7:100464600-100465400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr7:100464600-100465400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
33	chr7:100464600-100465600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr7:100464600-100465600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr7:100464600-100465600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr7:100464600-100465800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:100464600-100465800	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr7:100464600-100465800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr7:100464600-100465800	Active TSS	Aorta	Aorta
40	chr7:100464600-100465800	Active TSS	Left Ventricle	heart
41	chr7:100464600-100465800	Active TSS	Rectal Smooth Muscle	rectum
42	chr7:100464600-100465800	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr7:100464600-100466000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr7:100464600-100466000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr7:100464600-100466000	Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr7:100464600-100466200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr7:100464600-100466200	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr7:100464600-100466400	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr7:100464600-100466400	Active TSS	H9 Cell Line	embryonic stem cell
50	chr7:100464600-100466400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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