Variant report

Variant	rs67147615
Chromosome Location	chr7:100167002-100167003
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	ELF1	chr7:100166533-100168319	GM12878	blood:	n/a	chr7:100167577-100167589
2	POLR2A	chr7:100164566-100167757	K562	blood:	n/a	n/a
3	CTCF	chr7:100166963-100167306	GM12878	blood:	n/a	n/a
4	POLR2A	chr7:100163833-100176987	HepG2	liver:	n/a	n/a
5	NFATC1	chr7:100164689-100168128	GM12878	blood:	n/a	n/a
6	POLR2A	chr7:100164603-100168250	HepG2	liver:	n/a	n/a
7	POLR2A	chr7:100165760-100168202	HUVEC	blood vessel:	n/a	n/a
8	MXI1	chr7:100166918-100168199	IMR90	lung:	n/a	chr7:100167256-100167271
9	MXI1	chr7:100166957-100168115	HepG2	liver:	n/a	chr7:100167256-100167271
10	POLR2A	chr7:100163798-100168114	K562	blood:	n/a	n/a
11	POLR2A	chr7:100165011-100168250	GM12878	blood:	n/a	n/a
12	YY1	chr7:100166987-100167371	K562	blood:	n/a	n/a
13	RAD21	chr7:100166982-100167289	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr7:100166165-100167119	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr7:100164708-100168144	GM18505	blood:	n/a	n/a
16	POLR2A	chr7:100166724-100168227	GM12878	blood:	n/a	n/a
17	CTCF	chr7:100166897-100167341	K562	blood:	n/a	n/a
18	BCL3	chr7:100166114-100168265	GM12878	blood:	n/a	chr7:100167721-100167734 chr7:100166126-100166135 chr7:100166367-100166376
19	TEAD4	chr7:100165254-100168250	HepG2	liver:	n/a	n/a
20	POLR2A	chr7:100166909-100167425	HCT-116	colon:	n/a	n/a
21	POLR2A	chr7:100166926-100168223	GM12892	blood:	n/a	n/a
22	CTCF	chr7:100166990-100167288	H1-hESC	embryonic stem cell:	n/a	n/a
23	RUNX3	chr7:100166707-100168312	GM12878	blood:	n/a	n/a
24	YY1	chr7:100167002-100167342	H1-hESC	embryonic stem cell:	n/a	n/a
25	HDAC2	chr7:100166974-100167490	HepG2	liver:	n/a	n/a
26	POLR2A	chr7:100166592-100168165	GM12891	blood:	n/a	n/a
27	POLR2A	chr7:100166067-100168092	HUVEC	blood vessel:	n/a	n/a
28	CTCF	chr7:100166980-100167130	HUVEC	blood vessel:	n/a	n/a
29	CTCF	chr7:100166940-100167090	HAc	cerebellar:	n/a	n/a
30	SMC3	chr7:100166967-100167357	K562	blood:	n/a	n/a
31	STAT5A	chr7:100164915-100168333	GM12878	blood:	n/a	chr7:100165938-100165950 chr7:100165943-100165955 chr7:100167613-100167625 chr7:100166761-100166768
32	GABPA	chr7:100166878-100167316	H1-hESC	embryonic stem cell:	n/a	n/a
33	ELF1	chr7:100166637-100167637	HepG2	liver:	n/a	chr7:100167577-100167589
34	SIN3AK20	chr7:100166999-100167417	K562	blood:	n/a	n/a
35	CTCF	chr7:100166944-100167318	K562	blood:	n/a	n/a
36	MBD4	chr7:100164576-100169895	HepG2	liver:	n/a	n/a
37	YY1	chr7:100166726-100168325	HepG2	liver:	n/a	chr7:100167575-100167586 chr7:100167570-100167584 chr7:100167721-100167730 chr7:100167721-100167735 chr7:100167718-100167732 chr7:100167715-100167729
38	MAX	chr7:100164909-100168280	HepG2	liver:	n/a	chr7:100166012-100166021 chr7:100166012-100166021 chr7:100166011-100166021 chr7:100166012-100166021 chr7:100166014-100166023 chr7:100165952-100165962 chr7:100166343-100166352 chr7:100165981-100165991
39	CTCF	chr7:100166999-100167323	GM12891	blood:	n/a	n/a
40	JUND	chr7:100166902-100168276	HepG2	liver:	n/a	n/a
41	HEY1	chr7:100166891-100167697	HepG2	liver:	n/a	n/a
42	CTCF	chr7:100166991-100167250	A549	lung:	n/a	n/a
43	ELF1	chr7:100166783-100167533	HepG2	liver:	n/a	n/a
44	POLR2A	chr7:100164983-100168251	GM12878	blood:	n/a	n/a
45	USF1	chr7:100167002-100167439	K562	blood:	n/a	n/a
46	RAD21	chr7:100166980-100167268	H1-hESC	embryonic stem cell:	n/a	n/a
47	PML	chr7:100164911-100168292	GM12878	blood:	n/a	n/a
48	CTCF	chr7:100167000-100167150	NHEK	skin:	n/a	n/a
49	MAX	chr7:100166930-100167417	K562	blood:	n/a	n/a
50	MTA3	chr7:100164761-100168316	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:100164645..100167168-chr7:100274291..100277029,2	MCF-7	breast:
2	chr7:100135274..100138223-chr7:100165794..100167927,2	MCF-7	breast:
3	chr7:100164565..100167457-chr7:100344225..100346169,2	K562	blood:
4	chr7:100166742..100169680-chr7:100229325..100230854,2	MCF-7	breast:
5	chr7:100023646..100028399-chr7:100166149..100169452,5	K562	blood:
6	chr7:100136389..100138231-chr7:100164373..100167646,4	MCF-7	breast:
7	chr7:100135710..100139332-chr7:100164432..100167649,4	K562	blood:
8	chr7:100025402..100027962-chr7:100165683..100167743,2	MCF-7	breast:
9	chr7:100166949..100169770-chr7:100238447..100240674,2	K562	blood:
10	chr7:99998151..99998794-chr7:100166668..100167627,2	K562	blood:
11	chr7:100164021..100167262-chr7:100491733..100494346,3	K562	blood:

Variant related genes	Relation type
ENSG00000184414	TF binding region
ENSG00000146834	Chromatin interaction
ENSG00000106327	Chromatin interaction
ENSG00000087085	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000106351	Chromatin interaction
ENSG00000172354	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11972116	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11977607	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11978096	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11978967	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12154919	0.85[EUR][1000 genomes]
rs12216707	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2406243	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34440977	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56307653	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58509206	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60668677	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60743967	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61309832	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61318457	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67535650	0.88[EUR][1000 genomes]
rs6970240	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73154884	0.86[EUR][1000 genomes]
rs73154887	0.86[EUR][1000 genomes]
rs73154891	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73154894	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73154895	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73154897	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73154902	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73156207	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73156208	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73156210	0.90[EUR][1000 genomes]
rs73156211	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73711133	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73711136	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73711137	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7784759	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7799695	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv888776	chr7:100014711-100198386	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	297 gene(s)	inside rSNPs	diseases
3	nsv888777	chr7:100014711-100221867	Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
4	nsv888778	chr7:100014711-100236593	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	310 gene(s)	inside rSNPs	diseases
5	nsv888779	chr7:100014711-100313420	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	321 gene(s)	inside rSNPs	diseases
6	nsv888780	chr7:100032665-100198386	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS 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 target site	81 gene(s)	inside rSNPs	diseases
7	nsv888782	chr7:100064719-100236593	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
8	nsv888785	chr7:100141861-100313420	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
9	nsv888786	chr7:100159567-100313420	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
10	nsv888787	chr7:100161557-100179857	ZNF genes & repeats Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases
11	nsv888788	chr7:100161557-100186066	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	52 gene(s)	inside rSNPs	diseases
12	nsv831072	chr7:100162503-100362835	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
13	nsv888789	chr7:100166585-100178915	Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs67147615	SAP25	cis	Artery Tibial	GTEx
rs67147615	LRCH4	cis	Esophagus Muscularis	GTEx
rs67147615	SAP25	cis	Thyroid	GTEx
rs67147615	SAP25	cis	Nerve Tibial	GTEx
rs67147615	SAP25	cis	Esophagus Muscularis	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100145200-100167400	Weak transcription	HSMM	muscle
2	chr7:100146600-100167200	Weak transcription	Fetal Heart	heart
3	chr7:100151400-100167400	Weak transcription	Psoas Muscle	Psoas
4	chr7:100154400-100167400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr7:100154400-100167400	Weak transcription	HMEC	breast
6	chr7:100154600-100173600	Weak transcription	HSMMtube	muscle
7	chr7:100155000-100167200	Weak transcription	Osteobl	bone
8	chr7:100157800-100169600	Weak transcription	Hela-S3	cervix
9	chr7:100158200-100167200	Weak transcription	Right Atrium	heart
10	chr7:100158800-100167600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr7:100159800-100167400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr7:100160800-100172800	Weak transcription	Aorta	Aorta
13	chr7:100161000-100167200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr7:100161400-100167800	Weak transcription	NHLF	lung
15	chr7:100164000-100167600	Enhancers	Pancreas	Pancrea
16	chr7:100164200-100167200	Weak transcription	Thymus	Thymus
17	chr7:100164400-100167400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:100164600-100167200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr7:100164600-100169000	Enhancers	Placenta	Placenta
20	chr7:100164800-100167200	Enhancers	Primary B cells from peripheral blood	blood
21	chr7:100164800-100167200	Flanking Active TSS	HepG2	liver
22	chr7:100164800-100168000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr7:100165000-100167200	Enhancers	Primary T cells fromperipheralblood	blood
24	chr7:100165000-100167200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr7:100165000-100167200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr7:100165000-100167200	Enhancers	Duodenum Mucosa	Duodenum
27	chr7:100165000-100167200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr7:100165000-100167400	Enhancers	Primary B cells from cord blood	blood
29	chr7:100165000-100167400	Enhancers	GM12878-XiMat	blood
30	chr7:100165000-100167600	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr7:100165200-100167200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr7:100165200-100167200	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr7:100165200-100167200	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr7:100165200-100167200	Enhancers	Adipose Nuclei	Adipose
35	chr7:100165200-100167400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr7:100165200-100168800	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr7:100165400-100167200	Enhancers	Primary T cells from cord blood	blood
38	chr7:100165400-100167200	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr7:100165400-100167200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr7:100165400-100167200	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr7:100165400-100167200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr7:100165600-100167200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr7:100165600-100167200	Enhancers	Fetal Intestine Small	intestine
44	chr7:100165600-100167200	Weak transcription	NH-A	brain
45	chr7:100165600-100167400	Enhancers	Stomach Mucosa	stomach
46	chr7:100165600-100167600	Enhancers	Gastric	stomach
47	chr7:100165600-100168800	Enhancers	Primary hematopoietic stem cells	blood
48	chr7:100165600-100169600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr7:100165800-100167200	Enhancers	Brain Hippocampus Middle	brain
50	chr7:100165800-100167200	Enhancers	Rectal Mucosa Donor 31	rectum

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