Variant report

Variant	rs1197700
Chromosome Location	chr15:42186482-42186483
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:35)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:35 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:42186380-42186530	HMEC	breast:	n/a	n/a
2	ELF1	chr15:42186391-42187918	GM12878	blood:	n/a	chr15:42186941-42186953
3	ZNF263	chr15:42186114-42187973	HEK293-T-REx	kidney:	n/a	chr15:42186877-42186886
4	NR3C1	chr15:42186089-42186532	ECC-1	luminal epithelium:	n/a	n/a
5	YY1	chr15:42186072-42186526	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr15:42184705-42187956	ECC-1	luminal epithelium:	n/a	n/a
7	TCF12	chr15:42185817-42187923	ECC-1	luminal epithelium:	n/a	n/a
8	EP300	chr15:42185396-42188142	SK-N-SH	brain:	n/a	chr15:42187116-42187125
9	NFIC	chr15:42183898-42187893	ECC-1	luminal epithelium:	n/a	chr15:42184240-42184268
10	NFIC	chr15:42185515-42186758	ECC-1	luminal epithelium:	n/a	n/a
11	MAX	chr15:42186006-42186689	ECC-1	luminal epithelium:	n/a	chr15:42186304-42186314
12	ZBTB7A	chr15:42184792-42187816	ECC-1	luminal epithelium:	n/a	chr15:42186860-42186871 chr15:42185909-42185917
13	YY1	chr15:42185964-42186631	ECC-1	luminal epithelium:	n/a	n/a
14	ESR1	chr15:42186203-42186496	ECC-1	luminal epithelium:	n/a	n/a
15	EGR1	chr15:42186032-42186755	ECC-1	luminal epithelium:	n/a	chr15:42186471-42186481 chr15:42186470-42186481 chr15:42186470-42186481 chr15:42186304-42186319
16	TCF12	chr15:42186001-42187847	ECC-1	luminal epithelium:	n/a	n/a
17	ESR1	chr15:42186076-42186594	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr15:42186000-42187750	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr15:42185991-42189010	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr15:42186381-42187786	HUVEC	blood vessel:	n/a	n/a
21	EP300	chr15:42185929-42186772	ECC-1	luminal epithelium:	n/a	n/a
22	MAX	chr15:42186003-42186667	ECC-1	luminal epithelium:	n/a	chr15:42186304-42186314
23	RAD21	chr15:42186094-42186613	ECC-1	luminal epithelium:	n/a	n/a
24	TEAD4	chr15:42186020-42186740	ECC-1	luminal epithelium:	n/a	n/a
25	CTCF	chr15:42186360-42186510	HBMEC	blood vessel:	n/a	n/a
26	POLR2A	chr15:42185834-42189791	HUVEC	blood vessel:	n/a	n/a
27	ZBTB7A	chr15:42184766-42187747	ECC-1	luminal epithelium:	n/a	chr15:42186860-42186871 chr15:42185909-42185917
28	CTCF	chr15:42186360-42186510	HMEC	breast:	n/a	n/a
29	EP300	chr15:42185696-42187904	ECC-1	luminal epithelium:	n/a	chr15:42187116-42187125
30	ESR1	chr15:42186048-42186612	ECC-1	luminal epithelium:	n/a	n/a
31	EGR1	chr15:42186059-42187321	ECC-1	luminal epithelium:	n/a	chr15:42186989-42187000 chr15:42186471-42186481 chr15:42186470-42186481 chr15:42186470-42186481 chr15:42186304-42186319
32	POLR2A	chr15:42186003-42187823	HUVEC	blood vessel:	n/a	n/a
33	NR3C1	chr15:42186088-42186558	ECC-1	luminal epithelium:	n/a	n/a
34	CTCF	chr15:42186360-42186510	HepG2	liver:	n/a	n/a
35	TEAD4	chr15:42185967-42186580	ECC-1	luminal epithelium:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:42186473-42186523	NH-A	brain:	n/a
2	chr15:42186473-42186523	AG09319	gingival:	n/a
3	chr15:42186473-42186523	MCF-7	breast:	n/a
4	chr15:42186473-42186523	AG09309	skin:	n/a
5	chr15:42186473-42186523	IMR90	lung:	fetal
6	chr15:42186473-42186523	NB4	blood:	n/a
7	chr15:42186473-42186523	HRCEpiC	kidney:	n/a
8	chr15:42186473-42186523	BE2_C	brain:	n/a
9	chr15:42186473-42186523	HCF	heart:	n/a
10	chr15:42186473-42186523	ECC-1	luminal epithelium:	n/a
11	chr15:42186473-42186523	HPAEpiC	pulmonary alveolar:	n/a
12	chr15:42186473-42186523	GM12891	blood:	n/a
13	chr15:42186473-42186523	HEEpiC	esophagus:	n/a
14	chr15:42186473-42186523	AG04449	skin:	fetal
15	chr15:42186473-42186523	A549	lung:	n/a
16	chr15:42186473-42186523	HUVEC	blood vessel:	n/a
17	chr15:42186473-42186523	Jurkat	blood:	n/a
18	chr15:42186473-42186523	NT2-D1	testis:	n/a
19	chr15:42186473-42186523	GM19239	blood:	n/a
20	chr15:42186473-42186523	AG04450	lung:	fetal
21	chr15:42186473-42186523	MCF10A-Er-Src	breast:	n/a
22	chr15:42186473-42186523	GM06990	blood:	n/a
23	chr15:42186473-42186523	U87	brain:	n/a
24	chr15:42186473-42186523	SAEC	small airway:	n/a
25	chr15:42186473-42186523	HCM	heart:	n/a
26	chr15:42186473-42186523	PANC-1	pancreas:	n/a
27	chr15:42186473-42186523	ovcar-3	ovarian:	n/a
28	chr15:42186473-42186523	HL-60	blood:	n/a
29	chr15:42186473-42186523	Caco-2	colon:	n/a
30	chr15:42186473-42186523	SK-N-MC	brain:	n/a
31	chr15:42186473-42186523	GM12892	blood:	n/a
32	chr15:42186473-42186523	NHBE	bronchial:	n/a
33	chr15:42186473-42186523	GM12878	blood:	n/a
34	chr15:42186473-42186523	CMK	blood:	n/a
35	chr15:42186473-42186523	PrEC	prostate:	n/a
36	chr15:42186473-42186523	HRPEpiC	eye:	n/a
37	chr15:42186473-42186523	SKMC	muscle:	n/a
38	chr15:42186473-42186523	HAEpiC	amniotic membrane:	n/a
39	chr15:42186473-42186523	Hela-S3	cervix:	n/a
40	chr15:42186473-42186523	NHDF-neo	bronchial:	n/a
41	chr15:42186473-42186523	RPTEC	kidney:	n/a
42	chr15:42186473-42186523	HMEC	breast:	n/a
43	chr15:42186473-42186523	BJ	skin:	n/a
44	chr15:42186473-42186523	HepG2	liver:	n/a
45	chr15:42186473-42186523	HCPEpiC	choroid plexus:	n/a
46	chr15:42186473-42186523	T-47D	breast:	n/a
47	chr15:42186473-42186523	HRE	kidney:	n/a
48	chr15:42186473-42186523	AG10803	skin:	n/a
49	chr15:42186473-42186523	SK-N-SH	brain:	n/a
50	chr15:42186473-42186523	PFSK-1	brain:	n/a

No data

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-JMJD7-PLA2G4B-1	chr15:42184991-42187534	ENSG00000174171.3
2	lnc-JMJD7-PLA2G4B-2	chr15:42185134-42186566	NONHSAT041977

No data

Variant related genes	Relation type
ENSG00000174171	TF binding region
SPTBN5	TF binding region
ENSG00000174171	CpG island
SPTBN5	CpG island

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1197657	0.85[ASN][1000 genomes]
rs1197658	0.85[ASN][1000 genomes]
rs1197683	1.00[ASN][1000 genomes]
rs1197685	1.00[ASN][1000 genomes]
rs1197692	1.00[ASN][1000 genomes]
rs1197697	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1201690	1.00[ASN][1000 genomes]
rs1210795	0.87[ASW][hapmap];0.90[GIH][hapmap];0.84[MKK][hapmap];1.00[ASN][1000 genomes]
rs1211289	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs12916542	1.00[CHB][hapmap]
rs1672460	1.00[CHB][hapmap]
rs1704380	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv427958	chr15:42051317-42301283	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS 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 miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv904116	chr15:42076387-42229852	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1038393	chr15:42083574-42188035	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
5	esv1827003	chr15:42087505-42199076	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1041645	chr15:42095168-42186482	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1051200	chr15:42095168-42188035	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
8	nsv517631	chr15:42096926-42187492	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
9	nsv1051733	chr15:42098896-42186482	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
10	nsv1036153	chr15:42098896-42188035	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
11	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
12	nsv1048606	chr15:42101694-42192760	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
13	nsv904118	chr15:42103822-42207905	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
14	nsv904124	chr15:42109975-42207905	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
15	nsv9244	chr15:42110712-42208805	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
16	nsv904125	chr15:42119900-42210393	Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
17	nsv1050892	chr15:42128855-42186482	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
18	nsv1038933	chr15:42138456-42309087	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS 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	30 gene(s)	inside rSNPs	diseases
19	nsv904127	chr15:42142912-42207905	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
20	nsv904128	chr15:42147639-42207905	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
21	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
22	nsv904129	chr15:42162957-42207905	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
23	nsv1054728	chr15:42177772-42310009	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1197700	JMJD7-PLA2G4B	cis	cerebellum	SCAN
rs1197700	LPAR6	trans	lymphoblastoid	seeQTL
rs1197700	ZSCAN29	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42141200-42191200	Weak transcription	Aorta	Aorta
2	chr15:42174200-42186600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr15:42175800-42191000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr15:42175800-42191000	Weak transcription	Thymus	Thymus
5	chr15:42181200-42186600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr15:42182600-42187800	Enhancers	Fetal Muscle Leg	muscle
7	chr15:42183600-42187000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:42183600-42191200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr15:42183600-42191400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr15:42183600-42195800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:42183600-42196000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:42183800-42186600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr15:42183800-42187000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr15:42183800-42187600	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr15:42183800-42195800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:42184000-42188000	Enhancers	Fetal Heart	heart
17	chr15:42184200-42186800	Enhancers	Primary B cells from peripheral blood	blood
18	chr15:42184400-42188000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr15:42184400-42189600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr15:42184400-42192800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr15:42184600-42186800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr15:42184600-42187400	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr15:42184600-42187600	Enhancers	Colon Smooth Muscle	Colon
24	chr15:42184600-42187800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr15:42184600-42188000	Enhancers	Primary B cells from cord blood	blood
26	chr15:42184600-42188000	Enhancers	Primary hematopoietic stem cells	blood
27	chr15:42184600-42188000	Enhancers	Fetal Stomach	stomach
28	chr15:42184600-42188000	Enhancers	Fetal Thymus	thymus
29	chr15:42184800-42186600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr15:42184800-42186800	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr15:42184800-42187000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr15:42184800-42187600	Enhancers	Stomach Mucosa	stomach
33	chr15:42184800-42187800	Enhancers	Placenta Amnion	Placenta Amnion
34	chr15:42185000-42186800	Enhancers	Esophagus	oesophagus
35	chr15:42185000-42187400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
36	chr15:42185000-42187600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr15:42185000-42187600	Enhancers	Fetal Intestine Small	intestine
38	chr15:42185000-42187600	Enhancers	Gastric	stomach
39	chr15:42185000-42187800	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr15:42185000-42187800	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr15:42185400-42186600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr15:42185400-42186600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr15:42185400-42187000	Enhancers	Fetal Intestine Large	intestine
44	chr15:42185400-42188000	Enhancers	Pancreas	Pancrea
45	chr15:42185600-42186600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr15:42185600-42186600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr15:42185600-42186600	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr15:42185600-42187600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
49	chr15:42185600-42188000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr15:42185600-42188000	Enhancers	NH-A	brain

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