Variant report

Variant	rs7702843
Chromosome Location	chr5:1795377-1795378
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:1794019..1795658-chr5:2041608..2044062,2	MCF-7	breast:
2	chr5:1793350..1795860-chr5:1944846..1947402,2	MCF-7	breast:
3	chr5:1793765..1806799-chr5:1879445..1889322,45	MCF-7	breast:
4	chr5:1794905..1795739-chr7:139705398..139706186,2	HCT-116	colon:
5	chr5:1787615..1789328-chr5:1793761..1797388,3	K562	blood:

Variant related genes	Relation type
ENSG00000113430	Chromatin interaction
ENSG00000249326	Chromatin interaction
ENSG00000249116	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11133910	0.95[CHB][hapmap];0.84[JPT][hapmap];0.94[ASN][1000 genomes]
rs11133911	0.91[ASN][1000 genomes]
rs11133912	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13187162	0.93[ASN][1000 genomes]
rs1845288	0.94[ASN][1000 genomes]
rs1873926	0.91[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs2242412	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2276986	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2291944	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34233926	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35380881	0.91[ASN][1000 genomes]
rs3756343	0.95[CHB][hapmap];0.91[CHD][hapmap];0.80[JPT][hapmap];0.92[ASN][1000 genomes]
rs3756345	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs3756346	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs3776141	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs3776142	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs3776143	0.96[ASN][1000 genomes]
rs3776144	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3776145	0.94[ASN][1000 genomes]
rs3776146	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3776149	0.95[CHB][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs3822364	0.96[ASN][1000 genomes]
rs4147769	0.94[ASN][1000 genomes]
rs4147770	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4147772	0.95[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs4147773	0.95[CHB][hapmap];0.84[JPT][hapmap];0.94[ASN][1000 genomes]
rs4975845	0.82[ASW][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs4975848	0.95[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs4975849	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs4975851	0.95[CHB][hapmap];0.91[ASN][1000 genomes]
rs4975852	0.95[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs4975853	0.95[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs55883912	0.92[ASN][1000 genomes]
rs6555012	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6863367	0.92[ASN][1000 genomes]
rs972890	0.95[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs972891	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs972892	0.95[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs974722	0.96[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	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
3	nsv1034552	chr5:1658338-1856553	Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
4	nsv537606	chr5:1658338-1856553	Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
5	nsv1033147	chr5:1717303-1815821	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
6	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv1020703	chr5:1724199-1814288	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
8	nsv537608	chr5:1724199-1814288	Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
9	nsv1024133	chr5:1736691-1826510	Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
10	nsv537609	chr5:1736691-1826510	Genic enhancers Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7702843	LRTM1	trans	brain	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1785200-1796000	Weak transcription	Thymus	Thymus
2	chr5:1786800-1796000	Weak transcription	Gastric	stomach
3	chr5:1789200-1796400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:1789200-1796400	Weak transcription	Esophagus	oesophagus
5	chr5:1789400-1795600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:1790200-1795600	Enhancers	Fetal Muscle Leg	muscle
7	chr5:1790200-1796200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr5:1790400-1795600	Enhancers	NHDF-Ad	bronchial
9	chr5:1790400-1796400	Weak transcription	Brain Anterior Caudate	brain
10	chr5:1790400-1796800	Weak transcription	Brain Hippocampus Middle	brain
11	chr5:1790600-1796200	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr5:1790600-1796400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr5:1790600-1796600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr5:1790600-1797000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:1790600-1797000	Weak transcription	Fetal Lung	lung
16	chr5:1790600-1797800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr5:1790800-1796000	Weak transcription	Brain Substantia Nigra	brain
18	chr5:1790800-1796200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr5:1790800-1796400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr5:1790800-1796600	Weak transcription	Adipose Nuclei	Adipose
21	chr5:1790800-1797000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:1791000-1795600	Enhancers	Osteobl	bone
23	chr5:1791000-1796000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr5:1791000-1796200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:1791000-1796200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:1791000-1796400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr5:1791000-1796400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr5:1791000-1796600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr5:1791000-1796600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr5:1791000-1798800	Weak transcription	Fetal Brain Male	brain
31	chr5:1791000-1800200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr5:1791200-1795800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr5:1791200-1796200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr5:1791400-1796600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr5:1791600-1795400	Weak transcription	Brain Germinal Matrix	brain
36	chr5:1791600-1796600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr5:1792200-1795800	Weak transcription	Fetal Intestine Small	intestine
38	chr5:1792400-1795400	Enhancers	HMEC	breast
39	chr5:1792400-1797600	Weak transcription	Fetal Kidney	kidney
40	chr5:1792600-1795400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr5:1792800-1796800	Weak transcription	Fetal Intestine Large	intestine
42	chr5:1793000-1796400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr5:1793000-1796800	Weak transcription	K562	blood
44	chr5:1793200-1795400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr5:1793200-1796200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr5:1793200-1798800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr5:1793400-1795600	Enhancers	NH-A	brain
48	chr5:1793400-1796400	Weak transcription	Dnd41	blood
49	chr5:1793400-1797000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr5:1793600-1795400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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