Variant report

Variant	rs12442149
Chromosome Location	chr15:99640962-99640963
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	CTCF	chr15:99640880-99641030	GM12869	blood:	n/a	chr15:99640941-99640957 chr15:99641021-99641030 chr15:99640940-99640953
2	RAD21	chr15:99640794-99641063	GM12878	blood:	n/a	n/a
3	RAD21	chr15:99640768-99641162	HepG2	liver:	n/a	n/a
4	CTCF	chr15:99640820-99641098	HUVEC	blood vessel:	n/a	chr15:99640941-99640957 chr15:99641021-99641030 chr15:99640940-99640953
5	TEAD4	chr15:99640750-99641125	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr15:99640860-99641010	GM12865	blood:	n/a	chr15:99640941-99640957 chr15:99640940-99640953
7	EP300	chr15:99640633-99641125	A549	lung:	n/a	chr15:99640800-99640816 chr15:99640742-99640758 chr15:99640878-99640894
8	CTCF	chr15:99640860-99641010	HMEC	breast:	n/a	chr15:99640941-99640957 chr15:99640940-99640953
9	CTCF	chr15:99640780-99641105	GM19240	blood:	n/a	chr15:99640941-99640957 chr15:99641021-99641030 chr15:99640940-99640953
10	RAD21	chr15:99640770-99641169	HepG2	liver:	n/a	n/a
11	BRCA1	chr15:99640686-99641119	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAX	chr15:99640687-99641219	A549	lung:	n/a	n/a
13	CTCF	chr15:99640800-99641097	GM12878	blood:	n/a	chr15:99640941-99640957 chr15:99641021-99641030 chr15:99640940-99640953
14	MYC	chr15:99640902-99641013	MCF10A-Er-Src	breast:	n/a	n/a
15	CTCF	chr15:99640676-99641109	T-47D	breast:	n/a	chr15:99640941-99640957 chr15:99641021-99641030 chr15:99640940-99640953
16	CTCF	chr15:99640880-99641030	AG04449	skin:	n/a	chr15:99640941-99640957 chr15:99641021-99641030 chr15:99640940-99640953
17	CTCF	chr15:99640860-99641010	HRPEpiC	eye:	n/a	chr15:99640941-99640957 chr15:99640940-99640953
18	CTCF	chr15:99640860-99641010	GM12866	blood:	n/a	chr15:99640941-99640957 chr15:99640940-99640953
19	MAZ	chr15:99640788-99641036	GM12878	blood:	n/a	n/a
20	GTF2F1	chr15:99640811-99641082	Hela-S3	cervix:	n/a	n/a
21	CTCFL	chr15:99640906-99641037	K562	blood:	n/a	n/a
22	CTCF	chr15:99640880-99641030	HUVEC	blood vessel:	n/a	chr15:99640941-99640957 chr15:99641021-99641030 chr15:99640940-99640953
23	CTCF	chr15:99640840-99640990	GM12875	blood:	n/a	chr15:99640941-99640957 chr15:99640940-99640953
24	RAD21	chr15:99640765-99641074	K562	blood:	n/a	n/a
25	CTCF	chr15:99640860-99641010	AG09309	skin:	n/a	chr15:99640941-99640957 chr15:99640940-99640953
26	CTCF	chr15:99640880-99641030	GM12873	blood:	n/a	chr15:99640941-99640957 chr15:99641021-99641030 chr15:99640940-99640953
27	RCOR1	chr15:99640531-99641206	IMR90	lung:	n/a	n/a
28	RAD21	chr15:99640592-99641290	A549	lung:	n/a	n/a
29	CTCF	chr15:99640791-99641037	SK-N-SH_RA	brain:	n/a	chr15:99640941-99640957 chr15:99641021-99641030 chr15:99640940-99640953
30	CTCF	chr15:99640880-99641030	AG09319	gingival:	n/a	chr15:99640941-99640957 chr15:99641021-99641030 chr15:99640940-99640953
31	CTCF	chr15:99640810-99641068	LNCaP	prostate:	n/a	chr15:99640941-99640957 chr15:99641021-99641030 chr15:99640940-99640953
32	CTCF	chr15:99640685-99641153	H1-hESC	embryonic stem cell:	n/a	chr15:99640941-99640957 chr15:99641021-99641030 chr15:99640940-99640953
33	MAX	chr15:99640791-99641001	K562	blood:	n/a	n/a
34	STAT1	chr15:99640789-99640977	GM12878	blood:	n/a	n/a
35	CTCF	chr15:99640880-99641030	GM12865	blood:	n/a	chr15:99640941-99640957 chr15:99641021-99641030 chr15:99640940-99640953
36	RAD21	chr15:99640431-99641377	SK-N-SH	brain:	n/a	chr15:99640586-99640599
37	CTCF	chr15:99640789-99641082	GM10266	blood:	n/a	chr15:99640941-99640957 chr15:99641021-99641030 chr15:99640940-99640953
38	CTCF	chr15:99640880-99641030	HMEC	breast:	n/a	chr15:99640941-99640957 chr15:99641021-99641030 chr15:99640940-99640953
39	CTCF	chr15:99640818-99641085	Hela-S3	cervix:	n/a	chr15:99640941-99640957 chr15:99641021-99641030 chr15:99640940-99640953
40	CTCF	chr15:99640789-99641061	A549	lung:	n/a	chr15:99640941-99640957 chr15:99641021-99641030 chr15:99640940-99640953
41	CTCF	chr15:99640800-99641100	NHEK	skin:	n/a	chr15:99640941-99640957 chr15:99641021-99641030 chr15:99640940-99640953
42	RCOR1	chr15:99640797-99641052	HepG2	liver:	n/a	n/a
43	CTCF	chr15:99640678-99641250	HCT-116	colon:	n/a	chr15:99640941-99640957 chr15:99641021-99641030 chr15:99640940-99640953
44	ELF1	chr15:99640595-99641092	GM12878	blood:	n/a	n/a
45	YY1	chr15:99640815-99641091	GM12878	blood:	n/a	chr15:99640874-99640885
46	CTCF	chr15:99640880-99641030	WERI-Rb-1	eye:	n/a	chr15:99640941-99640957 chr15:99641021-99641030 chr15:99640940-99640953
47	CTCF	chr15:99640900-99641050	NHEK	skin:	n/a	chr15:99640941-99640957 chr15:99641021-99641030 chr15:99640940-99640953
48	GATA3	chr15:99640752-99641066	T-47D	breast:	n/a	chr15:99640942-99640952
49	ZNF143	chr15:99640745-99641134	GM12878	blood:	n/a	n/a
50	JUND	chr15:99640806-99641125	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:99640578..99641378-chr15:99747586..99748139,3	MCF-7	breast:
2	chr15:99640023..99641527-chr15:99752943..99754403,15	MCF-7	breast:
3	chr15:99640195..99641427-chr15:99752886..99754076,8	MCF-7	breast:
4	chr15:99640493..99643372-chr15:99648105..99650704,2	MCF-7	breast:
5	chr15:99640426..99641482-chr15:99753072..99754322,8	K562	blood:
6	chr15:99640796..99641313-chr15:99752001..99752808,2	MCF-7	breast:
7	chr15:99634162..99637138-chr15:99639706..99641886,2	MCF-7	breast:
8	chr15:99639780..99642328-chr15:99644918..99646902,2	MCF-7	breast:
9	chr15:99640854..99641425-chr15:99791150..99792070,2	K562	blood:
10	chr15:99639243..99641590-chr15:99753533..99755577,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SYNM-1	chr15:99638610-99641439	XLOC_011380
2	lnc-PGPEP1L-1	chr15:99640926-99641040	XLOC_011607
3	lnc-PGPEP1L-1	chr15:99640926-99641054	ENSG00000259475.1

Variant related genes	Relation type
SYNM	TF binding region
ENSG00000182253	Chromatin interaction
ENSG00000259475	Chromatin interaction
ENSG00000103852	Chromatin interaction
ENSG00000168904	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12440489	0.88[ASN][1000 genomes]
rs4965213	0.88[ASN][1000 genomes]
rs7496161	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS 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 miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats 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	60 gene(s)	inside rSNPs	diseases
4	nsv533375	chr15:99443534-99696221	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1050982	chr15:99450004-99725825	Enhancers Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv530685	chr15:99452377-99713365	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active 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	26 gene(s)	inside rSNPs	diseases
7	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv1045124	chr15:99504843-99847210	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv1038870	chr15:99510479-99768374	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
12	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
13	nsv904544	chr15:99524865-99655744	Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
14	nsv1051782	chr15:99621061-99792967	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
15	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
16	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
17	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
18	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
19	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99640200-99641000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
2	chr15:99640400-99641000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
3	chr15:99640400-99641000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:99640400-99641000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:99640400-99641000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr15:99640400-99641000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr15:99640400-99641000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
8	chr15:99640400-99641000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
9	chr15:99640400-99641000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
10	chr15:99640400-99641000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
11	chr15:99640400-99641000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr15:99640400-99641000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:99640400-99641000	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:99640400-99641000	Active TSS	Brain Angular Gyrus	brain
15	chr15:99640400-99641000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr15:99640400-99641000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
17	chr15:99640400-99641000	Bivalent/Poised TSS	Fetal Stomach	stomach
18	chr15:99640400-99641000	Bivalent Enhancer	Fetal Thymus	thymus
19	chr15:99640400-99641000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
20	chr15:99640400-99641000	Bivalent/Poised TSS	NH-A	brain
21	chr15:99640400-99641000	Bivalent/Poised TSS	Osteobl	bone
22	chr15:99640400-99641200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
23	chr15:99640400-99641200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
24	chr15:99640400-99641200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:99640400-99641200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr15:99640400-99641200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
27	chr15:99640400-99641200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr15:99640400-99641200	Active TSS	Brain Anterior Caudate	brain
29	chr15:99640400-99641200	Active TSS	Brain Cingulate Gyrus	brain
30	chr15:99640400-99641200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
31	chr15:99640400-99641200	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr15:99640400-99641200	Bivalent Enhancer	Stomach Mucosa	stomach
33	chr15:99640400-99641200	Flanking Active TSS	A549	lung
34	chr15:99640400-99641200	Active TSS	HSMM	muscle
35	chr15:99640400-99641200	Bivalent/Poised TSS	NHLF	lung
36	chr15:99640600-99641000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr15:99640600-99641000	Active TSS	H9 Cell Line	embryonic stem cell
38	chr15:99640600-99641000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr15:99640600-99641000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr15:99640600-99641000	Bivalent Enhancer	Primary B cells from cord blood	blood
41	chr15:99640600-99641000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
42	chr15:99640600-99641000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
43	chr15:99640600-99641000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr15:99640600-99641000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr15:99640600-99641000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr15:99640600-99641000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:99640600-99641000	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr15:99640600-99641000	Active TSS	Colon Smooth Muscle	Colon
49	chr15:99640600-99641000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
50	chr15:99640600-99641000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum

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