Variant report

Variant	rs73408579
Chromosome Location	chr15:42187041-42187042
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	RAD21	chr15:42186940-42187179	HepG2	liver:	n/a	n/a
2	ELF1	chr15:42186391-42187918	GM12878	blood:	n/a	chr15:42186941-42186953
3	CTCF	chr15:42186940-42187210	GM19238	blood:	n/a	n/a
4	CTCF	chr15:42186960-42187110	HBMEC	blood vessel:	n/a	n/a
5	PAX5	chr15:42186883-42187394	GM12878	blood:	n/a	chr15:42187148-42187166
6	CTCF	chr15:42187000-42187150	GM12873	blood:	n/a	n/a
7	CTCF	chr15:42186940-42187090	HMF	breast:	n/a	n/a
8	POLR2A	chr15:42186852-42187767	GM12892	blood:	n/a	n/a
9	CTCF	chr15:42186960-42187110	HMEC	breast:	n/a	n/a
10	CTCF	chr15:42187000-42187150	GM12864	blood:	n/a	n/a
11	HDAC2	chr15:42186979-42187189	K562	blood:	n/a	n/a
12	CTCF	chr15:42186980-42187130	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr15:42186736-42187992	PANC-1	pancreas:	n/a	n/a
14	ZNF263	chr15:42186114-42187973	HEK293-T-REx	kidney:	n/a	chr15:42186877-42186886
15	CTCF	chr15:42186930-42187170	Gliobla	brain:	n/a	n/a
16	JUND	chr15:42186727-42187385	GM12878	blood:	n/a	chr15:42187115-42187126 chr15:42187117-42187126 chr15:42187115-42187127 chr15:42187116-42187125
17	CTCF	chr15:42186900-42187050	HA-sp	spinal cord:	n/a	n/a
18	TCF7L2	chr15:42186906-42187657	HCT-116	colon:	n/a	chr15:42187116-42187125
19	CTCF	chr15:42186980-42187130	BJ	skin:	n/a	n/a
20	POLR2A	chr15:42186840-42187880	PANC-1	pancreas:	n/a	n/a
21	CTCF	chr15:42186960-42187110	GM12872	blood:	n/a	n/a
22	NFATC1	chr15:42186880-42187262	GM12878	blood:	n/a	n/a
23	JUND	chr15:42186945-42187312	HepG2	liver:	n/a	chr15:42187115-42187126 chr15:42187117-42187126 chr15:42187115-42187127 chr15:42187116-42187125
24	ATF3	chr15:42187005-42187159	K562	blood:	n/a	n/a
25	RAD21	chr15:42186950-42187182	GM12878	blood:	n/a	n/a
26	MAX	chr15:42186925-42187233	K562	blood:	n/a	chr15:42187116-42187125
27	FOSL1	chr15:42186921-42187344	K562	blood:	n/a	chr15:42187117-42187126 chr15:42187115-42187127 chr15:42187116-42187125
28	CTCF	chr15:42186980-42187130	SAEC	small airway:	n/a	n/a
29	YY1	chr15:42186894-42187323	GM12892	blood:	n/a	chr15:42187135-42187149
30	FOXP2	chr15:42186918-42187643	PFSK-1	brain:	n/a	n/a
31	CTCF	chr15:42186960-42187110	AG10803	skin:	n/a	n/a
32	BHLHE40	chr15:42186993-42187298	GM12878	blood:	n/a	n/a
33	EBF1	chr15:42186943-42187335	GM12878	blood:	n/a	chr15:42187094-42187105
34	SMC3	chr15:42186990-42187229	GM12878	blood:	n/a	n/a
35	POLR2A	chr15:42184705-42187956	ECC-1	luminal epithelium:	n/a	n/a
36	RUNX3	chr15:42186865-42187369	GM12878	blood:	n/a	n/a
37	MAX	chr15:42186993-42187193	K562	blood:	n/a	chr15:42187116-42187125
38	RAD21	chr15:42186854-42187223	SK-N-SH_RA	brain:	n/a	n/a
39	RAD21	chr15:42186915-42187197	K562	blood:	n/a	n/a
40	E2F4	chr15:42186951-42187276	MCF10A-Er-Src	breast:	n/a	chr15:42187088-42187102
41	ATF2	chr15:42186885-42187315	GM12878	blood:	n/a	n/a
42	POLR2A	chr15:42186890-42188019	GM12878	blood:	n/a	n/a
43	FOS	chr15:42186954-42187265	MCF10A-Er-Src	breast:	n/a	chr15:42187117-42187126 chr15:42187115-42187127 chr15:42187116-42187125 chr15:42187115-42187126
44	CTCF	chr15:42186931-42187287	K562	blood:	n/a	n/a
45	TCF12	chr15:42185817-42187923	ECC-1	luminal epithelium:	n/a	n/a
46	EP300	chr15:42185396-42188142	SK-N-SH	brain:	n/a	chr15:42187116-42187125
47	CTCF	chr15:42186965-42187204	GM19239	blood:	n/a	n/a
48	SRF	chr15:42186870-42187606	ECC-1	luminal epithelium:	n/a	n/a
49	BATF	chr15:42186963-42187346	GM12878	blood:	n/a	chr15:42187113-42187124 chr15:42187114-42187124
50	YY1	chr15:42186879-42187690	ECC-1	luminal epithelium:	n/a	chr15:42187135-42187149

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:42187036-42187086	HIPEpiC	eye:	n/a
2	chr15:42187036-42187086	GM19239	blood:	n/a
3	chr15:42187036-42187086	BJ	skin:	n/a
4	chr15:42187036-42187086	AoSMC	blood vessel:	n/a
5	chr15:42187036-42187086	AG09319	gingival:	n/a
6	chr15:42187036-42187086	LNCaP	prostate:	n/a
7	chr15:42187036-42187086	HPAEpiC	pulmonary alveolar:	n/a
8	chr15:42187036-42187086	ECC-1	luminal epithelium:	n/a
9	chr15:42187036-42187086	T-47D	breast:	n/a
10	chr15:42187036-42187086	HNPCEpiC	eye:	n/a
11	chr15:42187036-42187086	H1-hESC	embryonic stem cell:	embryo
12	chr15:42187036-42187086	GM06990	blood:	n/a
13	chr15:42187036-42187086	NH-A	brain:	n/a
14	chr15:42187036-42187086	GM12892	blood:	n/a
15	chr15:42187036-42187086	NB4	blood:	n/a
16	chr15:42187036-42187086	Jurkat	blood:	n/a
17	chr15:42187036-42187086	AG04450	lung:	fetal
18	chr15:42187036-42187086	GM12878	blood:	n/a
19	chr15:42187036-42187086	SK-N-SH_RA	brain:	n/a
20	chr15:42187036-42187086	HAEpiC	amniotic membrane:	n/a
21	chr15:42187036-42187086	HL-60	blood:	n/a
22	chr15:42187036-42187086	SKMC	muscle:	n/a
23	chr15:42187036-42187086	HRPEpiC	eye:	n/a
24	chr15:42187036-42187086	HUVEC	blood vessel:	n/a
25	chr15:42187036-42187086	HEEpiC	esophagus:	n/a
26	chr15:42187036-42187086	NHDF-neo	bronchial:	n/a
27	chr15:42187036-42187086	HCT-116	colon:	n/a
28	chr15:42187036-42187086	Caco-2	colon:	n/a
29	chr15:42187036-42187086	HRCEpiC	kidney:	n/a
30	chr15:42187036-42187086	HCF	heart:	n/a
31	chr15:42187036-42187086	NHBE	bronchial:	n/a
32	chr15:42187036-42187086	PANC-1	pancreas:	n/a
33	chr15:42187036-42187086	ovcar-3	ovarian:	n/a
34	chr15:42187036-42187086	Hepatocyte	liver:	n/a
35	chr15:42187036-42187086	HMEC	breast:	n/a
36	chr15:42187036-42187086	BE2_C	brain:	n/a
37	chr15:42187036-42187086	U87	brain:	n/a
38	chr15:42187036-42187086	IMR90	lung:	fetal
39	chr15:42187036-42187086	PFSK-1	brain:	n/a
40	chr15:42187036-42187086	NT2-D1	testis:	n/a
41	chr15:42187036-42187086	MCF-7	breast:	n/a
42	chr15:42187036-42187086	K562	blood:	n/a
43	chr15:42187036-42187086	AG10803	skin:	n/a
44	chr15:42187036-42187086	MCF10A-Er-Src	breast:	n/a
45	chr15:42187036-42187086	PrEC	prostate:	n/a
46	chr15:42187036-42187086	HEK293	kidney:	embryo
47	chr15:42187036-42187086	SK-N-MC	brain:	n/a
48	chr15:42187036-42187086	ProgFib	skin:	n/a
49	chr15:42187036-42187086	GM12891	blood:	n/a
50	chr15:42187036-42187086	AG04449	skin:	fetal

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

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

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1025226	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1030418	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1648821	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648822	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16972234	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16972243	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16972244	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16972246	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1704395	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1704397	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899033	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899034	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55637254	0.89[ASN][1000 genomes]
rs56008456	0.82[ASN][1000 genomes]
rs56379301	0.89[ASN][1000 genomes]
rs61753871	0.90[ASN][1000 genomes]
rs8034110	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42141200-42191200	Weak transcription	Aorta	Aorta
2	chr15:42175800-42191000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr15:42175800-42191000	Weak transcription	Thymus	Thymus
4	chr15:42182600-42187800	Enhancers	Fetal Muscle Leg	muscle
5	chr15:42183600-42191200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr15:42183600-42191400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr15:42183600-42195800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr15:42183600-42196000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:42183800-42187600	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr15:42183800-42195800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:42184000-42188000	Enhancers	Fetal Heart	heart
12	chr15:42184400-42188000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr15:42184400-42189600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:42184400-42192800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr15:42184600-42187400	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr15:42184600-42187600	Enhancers	Colon Smooth Muscle	Colon
17	chr15:42184600-42187800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr15:42184600-42188000	Enhancers	Primary B cells from cord blood	blood
19	chr15:42184600-42188000	Enhancers	Primary hematopoietic stem cells	blood
20	chr15:42184600-42188000	Enhancers	Fetal Stomach	stomach
21	chr15:42184600-42188000	Enhancers	Fetal Thymus	thymus
22	chr15:42184800-42187600	Enhancers	Stomach Mucosa	stomach
23	chr15:42184800-42187800	Enhancers	Placenta Amnion	Placenta Amnion
24	chr15:42185000-42187400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
25	chr15:42185000-42187600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr15:42185000-42187600	Enhancers	Fetal Intestine Small	intestine
27	chr15:42185000-42187600	Enhancers	Gastric	stomach
28	chr15:42185000-42187800	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr15:42185000-42187800	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr15:42185400-42188000	Enhancers	Pancreas	Pancrea
31	chr15:42185600-42187600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
32	chr15:42185600-42188000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr15:42185600-42188000	Enhancers	NH-A	brain
34	chr15:42185800-42187400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr15:42185800-42187400	Flanking Active TSS	Left Ventricle	heart
36	chr15:42185800-42187400	Flanking Active TSS	Right Ventricle	heart
37	chr15:42186000-42187400	Enhancers	HSMM	muscle
38	chr15:42186000-42187400	Enhancers	HSMMtube	muscle
39	chr15:42186000-42187600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr15:42186000-42187600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr15:42186000-42188000	Enhancers	Lung	lung
42	chr15:42186200-42187400	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr15:42186200-42187400	Flanking Active TSS	HMEC	breast
44	chr15:42186200-42187600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:42186200-42187600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:42186200-42187600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr15:42186200-42187600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:42186200-42187600	Enhancers	Placenta	Placenta
49	chr15:42186200-42187600	Enhancers	Ovary	ovary
50	chr15:42186200-42187600	Enhancers	NHDF-Ad	bronchial

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