Variant report

Variant	rs1861001
Chromosome Location	chr7:120725502-120725503
allele	A/G
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	TCF12	chr7:120723773-120725585	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr7:120723060-120727184	K562	blood:	n/a	n/a
3	PML	chr7:120718354-120726378	K562	blood:	n/a	chr7:120719627-120719635 chr7:120725652-120725660 chr7:120724224-120724233 chr7:120723324-120723333
4	TCF12	chr7:120723920-120725652	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr7:120717974-120727688	K562	blood:	n/a	n/a
6	POLR2A	chr7:120725423-120725525	K562	blood:	n/a	n/a
7	IRF1	chr7:120725255-120725506	K562	blood:	n/a	n/a
8	POLR2A	chr7:120722969-120726383	K562	blood:	n/a	n/a
9	POLR2A	chr7:120716166-120738240	K562	blood:	n/a	n/a
10	FOSL2	chr7:120724578-120725602	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr7:120724469-120726114	K562	blood:	n/a	n/a
12	POLR2A	chr7:120724341-120725942	K562	blood:	n/a	n/a
13	JUND	chr7:120723709-120725566	SK-N-SH	brain:	n/a	chr7:120724224-120724231 chr7:120724223-120724231 chr7:120724223-120724231 chr7:120724222-120724232 chr7:120724222-120724232 chr7:120724222-120724232 chr7:120724222-120724232 chr7:120724084-120724095

No.	Distal block	Cell Line	Cell type
1	chr7:120674115..120676104-chr7:120725405..120727477,2	K562	blood:
2	chr7:120624020..120645873-chr7:120713358..120727138,77	K562	blood:
3	chr7:120589600..120593889-chr7:120719099..120726294,8	K562	blood:
4	chr7:120621518..120649031-chr7:120712706..120728931,108	K562	blood:
5	chr7:120589475..120592677-chr7:120719093..120725846,11	K562	blood:
6	chr7:120701678..120704158-chr7:120722578..120725881,3	K562	blood:
7	chr7:120724755..120727043-chr8:49082625..49084125,2	K562	blood:

Variant related genes	Relation type
RNA5SP241	TF binding region
ENSG00000071243	Chromatin interaction
ENSG00000106034	Chromatin interaction
ENSG00000202225	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10235232	0.90[CHB][hapmap]
rs10246521	0.85[CHB][hapmap]
rs10251139	0.85[CHB][hapmap]
rs10259383	0.85[CHB][hapmap]
rs10261671	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs10275439	0.91[CHB][hapmap]
rs1112208	0.85[CHB][hapmap]
rs12673968	1.00[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];0.95[ASN][1000 genomes]
rs12706314	0.84[CHB][hapmap]
rs12706318	0.90[CHB][hapmap]
rs13223036	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs13232048	0.91[CHB][hapmap]
rs13245690	0.92[CHB][hapmap]
rs1404268	0.83[CHB][hapmap]
rs1524498	0.85[CHB][hapmap]
rs1524503	0.83[CHB][hapmap]
rs1554635	0.80[ASN][1000 genomes]
rs1558541	0.85[CHB][hapmap]
rs1861000	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1917112	0.85[CHB][hapmap]
rs1917113	1.00[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];0.95[ASN][1000 genomes]
rs2037632	0.85[CHB][hapmap]
rs2110281	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2110282	0.95[ASN][1000 genomes]
rs2110283	0.98[ASN][1000 genomes]
rs2177578	0.85[CHB][hapmap]
rs2968345	1.00[CHB][hapmap];0.82[JPT][hapmap];0.98[ASN][1000 genomes]
rs2968349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6466767	1.00[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs6466769	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs6947453	0.92[CHB][hapmap]
rs6950680	0.92[CHB][hapmap]
rs6952113	0.92[CHB][hapmap]
rs6954757	1.00[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs6956201	0.94[ASN][1000 genomes]
rs6961525	0.94[ASN][1000 genomes]
rs7787044	0.82[CHB][hapmap]
rs7799790	0.83[CHB][hapmap]
rs7801723	0.92[CHB][hapmap]
rs798933	1.00[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs798934	0.95[ASN][1000 genomes]
rs798943	0.92[CHB][hapmap]
rs798949	0.85[CHB][hapmap]
rs872007	0.92[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831114	chr7:120595624-120804510	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv608327	chr7:120633006-120873078	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv2753621	chr7:120635049-120800049	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1023611	chr7:120638930-120881658	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1025430	chr7:120638930-121179289	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1030792	chr7:120662815-120917533	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1031282	chr7:120667937-120887301	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv539099	chr7:120667937-120887301	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1019025	chr7:120667937-120918696	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv539100	chr7:120667937-120918696	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv534342	chr7:120667938-120887300	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv889118	chr7:120683751-120800837	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv889119	chr7:120688463-120800837	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv889120	chr7:120691417-120800837	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv428506	chr7:120719434-120891759	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1861001	LMOD2	cis	parietal	SCAN
rs1861001	FLJ21986	cis	multi-tissue	Pritchard

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120711400-120790600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr7:120721600-120726200	Weak transcription	Primary B cells from peripheral blood	blood
3	chr7:120722800-120726200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr7:120722800-120726800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr7:120722800-120727400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr7:120723000-120726800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:120723200-120727000	Enhancers	Rectal Smooth Muscle	rectum
8	chr7:120724000-120731200	Genic enhancers	K562	blood
9	chr7:120724200-120726200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr7:120724400-120725600	Enhancers	Stomach Smooth Muscle	stomach
11	chr7:120724400-120725800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr7:120724400-120726800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr7:120724400-120727000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr7:120724400-120728200	Enhancers	Adipose Nuclei	Adipose
15	chr7:120724400-120739800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr7:120724600-120725800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr7:120724600-120725800	Flanking Active TSS	NHDF-Ad	bronchial
18	chr7:120724600-120726000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr7:120724600-120727000	Enhancers	Liver	Liver
20	chr7:120724600-120727000	Enhancers	Fetal Heart	heart
21	chr7:120724800-120725600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr7:120724800-120727200	Enhancers	Ovary	ovary
23	chr7:120725000-120725800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr7:120725000-120725800	Enhancers	Fetal Stomach	stomach
25	chr7:120725000-120726400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr7:120725200-120725600	Active TSS	Colon Smooth Muscle	Colon
27	chr7:120725200-120725800	Flanking Active TSS	HSMMtube	muscle
28	chr7:120725200-120726000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr7:120725400-120725600	Enhancers	Aorta	Aorta
30	chr7:120725400-120725600	Enhancers	HSMM	muscle
31	chr7:120725400-120725600	Enhancers	NHLF	lung
32	chr7:120725400-120726600	Weak transcription	Psoas Muscle	Psoas
33	chr7:120725400-120726800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr7:120725400-120727000	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr7:120725400-120727000	Enhancers	HMEC	breast
36	chr7:120725400-120727000	Enhancers	NH-A	brain
37	chr7:120725400-120727000	Enhancers	NHEK	skin
38	chr7:120725400-120727600	Enhancers	Osteobl	bone
39	chr7:120725400-120728600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr7:120725400-120735000	Weak transcription	Right Ventricle	heart
41	chr7:120725400-120739600	Weak transcription	Left Ventricle	heart

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