Variant report

Variant	rs12672544
Chromosome Location	chr7:65957485-65957486
allele	A/C
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	POLR2A	chr7:65957384-65959133	GM12892	blood:	n/a	n/a
2	POLR2A	chr7:65957368-65959212	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr7:65957366-65959244	GM12892	blood:	n/a	n/a
4	POLR2A	chr7:65957401-65959247	GM12878	blood:	n/a	n/a
5	POLR2A	chr7:65957428-65957953	K562	blood:	n/a	n/a
6	E2F6	chr7:65957447-65957724	K562	blood:	n/a	n/a
7	ZNF263	chr7:65957340-65957962	HEK293-T-REx	kidney:	n/a	chr7:65957735-65957744
8	POLR2A	chr7:65957378-65957918	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr7:65957278-65957766	K562	blood:	n/a	n/a
10	HEY1	chr7:65957269-65959241	K562	blood:	n/a	chr7:65958591-65958600 chr7:65958593-65958602
11	POLR2A	chr7:65957320-65959134	HepG2	liver:	n/a	n/a
12	POLR2A	chr7:65957415-65959198	GM12891	blood:	n/a	n/a
13	MAX	chr7:65957352-65958121	K562	blood:	n/a	n/a
14	POLR2A	chr7:65957379-65957921	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr7:65957482-65957594	MCF-7	breast:	n/a	n/a
16	MYC	chr7:65957435-65959271	K562	blood:	n/a	n/a
17	CTCF	chr7:65957318-65957722	K562	blood:	n/a	n/a
18	POLR2A	chr7:65957272-65959216	K562	blood:	n/a	n/a
19	POLR2A	chr7:65957267-65959337	GM12878	blood:	n/a	n/a
20	CBX3	chr7:65957329-65957917	K562	blood:	n/a	n/a
21	HEY1	chr7:65957313-65959518	K562	blood:	n/a	chr7:65958591-65958600 chr7:65958593-65958602
22	TAF1	chr7:65957422-65959258	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAX	chr7:65957449-65957801	K562	blood:	n/a	n/a
24	POLR2A	chr7:65957342-65959127	GM12891	blood:	n/a	n/a
25	POLR2A	chr7:65957426-65957938	GM12878	blood:	n/a	n/a
26	POLR2A	chr7:65957305-65959151	K562	blood:	n/a	n/a
27	POLR2A	chr7:65957416-65957792	GM12878	blood:	n/a	n/a
28	POLR2A	chr7:65955495-65959617	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr7:65957329-65959308	GM12892	blood:	n/a	n/a
30	CTCF	chr7:65957480-65957630	HepG2	liver:	n/a	n/a
31	POLR2A	chr7:65957188-65959928	K562	blood:	n/a	n/a
32	CTCF	chr7:65957405-65957632	K562	blood:	n/a	n/a
33	POLR2A	chr7:65957417-65957876	HepG2	liver:	n/a	n/a
34	POLR2A	chr7:65957310-65959683	K562	blood:	n/a	n/a
35	POLR2A	chr7:65957032-65959515	H1-hESC	embryonic stem cell:	n/a	n/a
36	ZNF143	chr7:65957444-65957498	K562	blood:	n/a	n/a
37	USF1	chr7:65957433-65957765	K562	blood:	n/a	chr7:65957611-65957622
38	CTCF	chr7:65957472-65957598	K562	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SBDS-5	chr7:65956408-65958553	NONHSAT121189

Variant related genes	Relation type
ENSG00000237310	TF binding region
ENSG00000230189	TF binding region
ENSG00000244510	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10950040	0.82[ASN][1000 genomes]
rs12667200	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12668859	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12672427	0.89[ASN][1000 genomes]
rs35459055	0.88[ASN][1000 genomes]
rs3735147	0.85[ASN][1000 genomes]
rs4718346	0.81[ASN][1000 genomes]
rs4718348	0.84[ASN][1000 genomes]
rs6460298	0.84[ASN][1000 genomes]
rs6945896	0.88[ASN][1000 genomes]
rs6952881	0.82[EUR][1000 genomes]
rs6960848	0.86[ASN][1000 genomes]
rs73148689	0.87[ASN][1000 genomes]
rs73150604	0.88[ASN][1000 genomes]
rs7810213	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1035107	chr7:65814901-66114919	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv538909	chr7:65814901-66114919	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv888326	chr7:65825257-66066999	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv482441	chr7:65885824-66061788	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv1027068	chr7:65901543-65991211	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	esv3447484	chr7:65909457-66033145	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
9	esv3377926	chr7:65934493-66051484	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
10	nsv888327	chr7:65938980-66029429	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
11	esv3423847	chr7:65941210-66054107	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
12	nsv981508	chr7:65941357-65958736	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65879200-65957600	Weak transcription	Psoas Muscle	Psoas
2	chr7:65905600-65957600	Weak transcription	Fetal Lung	lung
3	chr7:65911400-65957800	Weak transcription	Aorta	Aorta
4	chr7:65917000-65957800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr7:65925000-65957600	Weak transcription	Left Ventricle	heart
6	chr7:65927600-65957600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr7:65931200-65957600	Weak transcription	Right Ventricle	heart
8	chr7:65931400-65957800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr7:65935800-65957600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr7:65937200-65957600	Weak transcription	HSMMtube	muscle
11	chr7:65937600-65958000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr7:65937800-65957600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr7:65937800-65957800	Weak transcription	Fetal Kidney	kidney
14	chr7:65937800-65957800	Weak transcription	Small Intestine	intestine
15	chr7:65938200-65957600	Weak transcription	HSMM	muscle
16	chr7:65938800-65957600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr7:65939200-65957600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr7:65939400-65957600	Weak transcription	Brain Germinal Matrix	brain
19	chr7:65940400-65957600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr7:65940600-65957600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr7:65940800-65957600	Weak transcription	Brain Hippocampus Middle	brain
22	chr7:65940800-65957600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr7:65941000-65957600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr7:65941000-65957600	Weak transcription	Spleen	Spleen
25	chr7:65941400-65957600	Weak transcription	Colon Smooth Muscle	Colon
26	chr7:65941600-65957600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr7:65942800-65957600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr7:65943400-65957600	Weak transcription	GM12878-XiMat	blood
29	chr7:65943600-65957600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr7:65944000-65957600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr7:65944200-65957600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr7:65944200-65957600	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr7:65944200-65957800	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr7:65944400-65957600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr7:65944400-65957600	Weak transcription	Primary B cells from cord blood	blood
36	chr7:65944400-65957600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr7:65944600-65957600	Weak transcription	Brain Angular Gyrus	brain
38	chr7:65945200-65957600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr7:65945200-65957600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr7:65945200-65957600	Weak transcription	Lung	lung
41	chr7:65945400-65957600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr7:65945800-65957600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr7:65946200-65957600	Weak transcription	Fetal Intestine Large	intestine
44	chr7:65946200-65957600	Weak transcription	Ovary	ovary
45	chr7:65946600-65957600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr7:65946600-65957600	Weak transcription	Placenta	Placenta
47	chr7:65946800-65957600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr7:65947000-65957600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr7:65947200-65957600	Weak transcription	Brain Anterior Caudate	brain
50	chr7:65947400-65957600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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