Variant report

Variant	rs7614424
Chromosome Location	chr3:52566354-52566355
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52566230-52566461	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:52565978-52567545	U87	brain:	n/a	n/a
3	PML	chr3:52566246-52566991	GM12878	blood:	n/a	n/a
4	HEY1	chr3:52566338-52566977	HepG2	liver:	n/a	chr3:52566862-52566877
5	POLR2A	chr3:52565799-52567472	HepG2	liver:	n/a	n/a
6	NFIC	chr3:52566293-52566987	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr3:52566281-52567117	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:52566310-52567117	HepG2	liver:	n/a	n/a
9	ZNF263	chr3:52565804-52566531	HEK293-T-REx	kidney:	n/a	n/a
10	JUND	chr3:52566180-52566961	K562	blood:	n/a	n/a
11	NFIC	chr3:52566337-52566826	HepG2	liver:	n/a	n/a
12	POLR2A	chr3:52565761-52567641	U87	brain:	n/a	n/a
13	POLR2A	chr3:52566150-52567589	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr3:52565766-52567830	GM12878	blood:	n/a	n/a
15	POLR2A	chr3:52566239-52567771	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr3:52563182-52567206	K562	blood:	n/a	n/a
17	POLR2A	chr3:52560598-52572342	HepG2	liver:	n/a	n/a
18	POLR2A	chr3:52566307-52567716	IMR90	lung:	n/a	n/a
19	POLR2A	chr3:52565765-52567056	PFSK-1	brain:	n/a	n/a
20	POLR2A	chr3:52564917-52567026	SK-N-MC	brain:	n/a	n/a
21	POLR2A	chr3:52564832-52568664	K562	blood:	n/a	n/a
22	POLR2A	chr3:52566209-52568194	GM12878	blood:	n/a	n/a
23	MYBL2	chr3:52566346-52566825	HepG2	liver:	n/a	n/a
24	MXI1	chr3:52566005-52569515	SK-N-SH	brain:	n/a	chr3:52566058-52566067
25	POLR2A	chr3:52566225-52567744	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr3:52566323-52566777	HCT-116	colon:	n/a	n/a
27	POLR2A	chr3:52565227-52568334	HUVEC	blood vessel:	n/a	n/a
28	MAZ	chr3:52565612-52569076	IMR90	lung:	n/a	chr3:52566595-52566603
29	POLR2A	chr3:52564773-52569282	K562	blood:	n/a	n/a
30	POLR2A	chr3:52566225-52567085	GM12878	blood:	n/a	n/a
31	BACH1	chr3:52566195-52566380	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52489605..52491332-chr3:52564945..52566721,2	K562	blood:
2	chr3:52566165..52568026-chr3:52648479..52651083,2	K562	blood:
3	chr3:52508946..52511340-chr3:52565152..52566782,2	MCF-7	breast:
4	chr3:52504515..52506973-chr3:52565446..52568302,2	MCF-7	breast:
5	chr3:52555579..52557218-chr3:52564676..52566664,2	MCF-7	breast:
6	chr3:52503525..52506168-chr3:52566167..52568849,2	MCF-7	breast:
7	chr3:52311763..52314254-chr3:52566006..52568592,3	K562	blood:
8	chr3:52487897..52490713-chr3:52565636..52568320,3	K562	blood:

No data

Variant related genes	Relation type
SMIM4	TF binding region
NT5DC2	TF binding region
ENSG00000164091	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000010327	Chromatin interaction
ENSG00000114854	Chromatin interaction
ENSG00000163939	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11709658	1.00[JPT][hapmap]
rs13066389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13066644	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13086936	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap]
rs13099479	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs13326165	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17052326	1.00[YRI][hapmap]
rs2577828	1.00[YRI][hapmap]
rs2590840	1.00[YRI][hapmap]
rs34182518	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs34735556	0.82[ASN][1000 genomes]
rs35225119	0.82[ASN][1000 genomes]
rs35272104	0.82[ASN][1000 genomes]
rs35325270	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35371456	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35911561	0.91[CEU][hapmap];1.00[CHD][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]
rs3733043	1.00[JPT][hapmap]
rs4234635	1.00[YRI][hapmap]
rs4687545	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67749743	1.00[ASN][1000 genomes]
rs72947530	0.80[AFR][1000 genomes]
rs72947531	0.80[AFR][1000 genomes]
rs72947532	0.80[AFR][1000 genomes]
rs72947537	0.82[AFR][1000 genomes]
rs758801	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs758802	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644763	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	63 gene(s)	inside rSNPs	diseases
7	nsv590305	chr3:52535586-52569480	Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv590307	chr3:52540773-52572056	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv876795	chr3:52544470-52572056	Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
10	nsv876796	chr3:52549676-52572056	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7614424	TMEM110	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52550600-52566600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:52554800-52567200	Weak transcription	Aorta	Aorta
3	chr3:52556800-52566400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:52558400-52567000	Weak transcription	Small Intestine	intestine
5	chr3:52558600-52566600	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:52558800-52566400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:52558800-52566600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:52559000-52566800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:52559800-52566400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:52560200-52566600	Weak transcription	Liver	Liver
11	chr3:52560600-52566800	Weak transcription	HSMMtube	muscle
12	chr3:52562400-52566400	Weak transcription	Thymus	Thymus
13	chr3:52562600-52566600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:52562800-52566600	Enhancers	Fetal Heart	heart
15	chr3:52562800-52566600	Weak transcription	Gastric	stomach
16	chr3:52562800-52566600	Enhancers	Right Atrium	heart
17	chr3:52563000-52566800	Enhancers	Lung	lung
18	chr3:52563200-52566400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:52563200-52566600	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr3:52563400-52566600	Enhancers	Left Ventricle	heart
21	chr3:52563400-52566600	Enhancers	Right Ventricle	heart
22	chr3:52563600-52566400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:52563600-52566600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:52563800-52566400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:52563800-52566600	Enhancers	Fetal Brain Male	brain
26	chr3:52564000-52566600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:52564000-52566600	Enhancers	Placenta	Placenta
28	chr3:52564000-52566800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr3:52564000-52567200	Enhancers	Spleen	Spleen
30	chr3:52564400-52566800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:52564800-52566600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:52565200-52566400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:52565400-52566400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:52565400-52566400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:52565400-52566600	Enhancers	Brain Hippocampus Middle	brain
36	chr3:52565400-52566600	Enhancers	Ovary	ovary
37	chr3:52565400-52566600	Enhancers	Placenta Amnion	Placenta Amnion
38	chr3:52565400-52566600	Enhancers	NHEK	skin
39	chr3:52565600-52566400	Enhancers	H1 Cell Line	embryonic stem cell
40	chr3:52565600-52566600	Weak transcription	Psoas Muscle	Psoas
41	chr3:52565800-52566400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:52565800-52566400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
43	chr3:52565800-52566400	Enhancers	Fetal Thymus	thymus
44	chr3:52565800-52566600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:52565800-52566600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr3:52565800-52566600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:52565800-52566600	Flanking Active TSS	HepG2	liver
48	chr3:52565800-52566800	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr3:52565800-52566800	Flanking Active TSS	NH-A	brain
50	chr3:52565800-52566800	Flanking Active TSS	NHLF	lung

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