Variant report

Variant	rs7257789
Chromosome Location	chr19:36426667-36426668
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	CTCF	chr19:36426580-36426730	Caco-2	colon:	n/a	n/a
2	MAX	chr19:36426513-36427735	A549	lung:	n/a	chr19:36427314-36427324 chr19:36427421-36427431
3	GATA2	chr19:36426606-36427248	SH-SY5Y	brain:	n/a	chr19:36426733-36426740
4	REST	chr19:36426518-36428374	H1-neurons	neurons:	n/a	chr19:36426848-36426858 chr19:36427881-36427891
5	MXI1	chr19:36426391-36428778	SK-N-SH	brain:	n/a	n/a
6	MAZ	chr19:36426386-36427799	IMR90	lung:	n/a	chr19:36427314-36427324 chr19:36427421-36427431
7	MAX	chr19:36426662-36427644	MCF-7	breast:	n/a	chr19:36427314-36427324 chr19:36427421-36427431
8	POLR2A	chr19:36426663-36427545	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:36231818..36233362-chr19:36425701..36428426,2	MCF-7	breast:
2	chr19:36239375..36241509-chr19:36425781..36428099,2	MCF-7	breast:
3	chr19:36370775..36373541-chr19:36425672..36427378,2	MCF-7	breast:
4	chr19:36390062..36392033-chr19:36425677..36427196,2	MCF-7	breast:
5	chr19:36426653..36429173-chr19:36484778..36487537,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRFN3-1	chr19:36426595-36426684	NONHSAT065940
2	lnc-LRFN3-1	chr19:36426260-36426684	NONHSAT065939

Variant related genes	Relation type
LRFN3	TF binding region
ENSG00000267796	Chromatin interaction
ENSG00000205138	Chromatin interaction
ENSG00000126246	Chromatin interaction
ENSG00000243968	Chromatin interaction
ENSG00000167604	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10221461	0.85[ASN][1000 genomes]
rs10221486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1057265	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11878444	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11878880	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11879537	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11880785	1.00[CEU][hapmap]
rs11880835	0.93[ASN][1000 genomes]
rs11880859	0.93[ASN][1000 genomes]
rs11881157	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11882386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11883234	0.91[ASN][1000 genomes]
rs13382036	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2242590	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293756	0.93[ASN][1000 genomes]
rs230260	0.82[ASW][hapmap];0.83[YRI][hapmap]
rs34933126	0.86[EUR][1000 genomes]
rs376240	0.82[ASW][hapmap];0.83[YRI][hapmap]
rs55686886	0.93[ASN][1000 genomes]
rs56042927	0.93[ASN][1000 genomes]
rs56132631	0.83[ASN][1000 genomes]
rs56132838	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56187901	0.93[ASN][1000 genomes]
rs56230692	0.93[ASN][1000 genomes]
rs56744930	0.86[EUR][1000 genomes]
rs56922307	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57068163	0.95[EUR][1000 genomes]
rs57094555	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57516855	0.81[EUR][1000 genomes]
rs57785375	0.93[ASN][1000 genomes]
rs57962062	0.91[EUR][1000 genomes]
rs58161969	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58456578	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58504183	0.91[EUR][1000 genomes]
rs58551711	0.91[EUR][1000 genomes]
rs58768499	0.90[ASN][1000 genomes]
rs58976020	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59150589	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59151712	0.93[ASN][1000 genomes]
rs59399698	0.81[EUR][1000 genomes]
rs59416903	0.91[EUR][1000 genomes]
rs59534183	0.81[EUR][1000 genomes]
rs60073802	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60276253	0.93[ASN][1000 genomes]
rs60500471	0.93[ASN][1000 genomes]
rs60892678	0.93[ASN][1000 genomes]
rs60935148	0.91[EUR][1000 genomes]
rs61510077	0.88[ASN][1000 genomes]
rs61660311	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61672461	0.86[EUR][1000 genomes]
rs7245383	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[ASN][1000 genomes]
rs7246259	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7247000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7247246	0.86[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7247769	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[ASN][1000 genomes]
rs7248253	0.93[ASN][1000 genomes]
rs7248265	0.93[ASN][1000 genomes]
rs7249502	0.93[ASN][1000 genomes]
rs7249567	0.92[CHB][hapmap];0.88[CHD][hapmap]
rs7251380	0.93[ASN][1000 genomes]
rs7251422	0.85[ASN][1000 genomes]
rs7251879	0.82[ASW][hapmap];0.83[YRI][hapmap]
rs7252053	0.85[ASN][1000 genomes]
rs7252526	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7252572	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7252693	0.93[ASN][1000 genomes]
rs7252839	0.93[ASN][1000 genomes]
rs7253086	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7254298	0.93[ASN][1000 genomes]
rs7254335	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7254905	0.93[ASN][1000 genomes]
rs7254994	0.93[ASN][1000 genomes]
rs7255824	0.93[ASN][1000 genomes]
rs7256280	0.86[EUR][1000 genomes]
rs7256433	0.91[EUR][1000 genomes]
rs7256952	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7257911	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7258909	0.82[ASW][hapmap];0.83[YRI][hapmap]
rs7258914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7259892	0.93[ASN][1000 genomes]
rs73599539	0.95[EUR][1000 genomes]
rs73599540	0.95[EUR][1000 genomes]
rs73599546	0.95[EUR][1000 genomes]
rs73599554	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73599561	0.86[EUR][1000 genomes]
rs73599565	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73599577	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73599586	0.86[EUR][1000 genomes]
rs73599600	0.91[EUR][1000 genomes]
rs73599602	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73928364	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73928368	0.93[ASN][1000 genomes]
rs73928369	0.93[ASN][1000 genomes]
rs8110868	0.95[EUR][1000 genomes]
rs8113704	0.82[ASW][hapmap];0.82[YRI][hapmap]
rs879407	0.82[ASW][hapmap];0.83[YRI][hapmap]
rs909135	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs909136	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911638	chr19:36265508-36537959	Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS 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	114 gene(s)	inside rSNPs	diseases
4	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
5	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv833812	chr19:36331913-36507594	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv833813	chr19:36341181-36499431	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7257789	USF2	cis	lymphoblastoid	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36425600-36426800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:36426000-36426800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr19:36426000-36426800	Enhancers	Gastric	stomach
4	chr19:36426000-36427000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr19:36426000-36427200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr19:36426200-36426800	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr19:36426200-36427000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr19:36426400-36426800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:36426400-36426800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:36426400-36426800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr19:36426400-36426800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr19:36426400-36426800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr19:36426400-36426800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
14	chr19:36426400-36426800	Flanking Active TSS	Brain Germinal Matrix	brain
15	chr19:36426400-36426800	Flanking Active TSS	Fetal Brain Female	brain
16	chr19:36426400-36426800	Flanking Active TSS	Fetal Intestine Large	intestine
17	chr19:36426400-36426800	Bivalent Enhancer	Fetal Thymus	thymus
18	chr19:36426400-36427000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:36426400-36427000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr19:36426400-36427000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr19:36426400-36427000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr19:36426400-36427000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr19:36426400-36427000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr19:36426400-36427000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr19:36426400-36427000	Flanking Active TSS	Brain Anterior Caudate	brain
26	chr19:36426400-36427000	Flanking Active TSS	Fetal Muscle Leg	muscle
27	chr19:36426400-36427000	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr19:36426400-36427200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr19:36426400-36427200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr19:36426400-36427200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr19:36426400-36427200	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr19:36426400-36427200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr19:36426400-36427200	Flanking Active TSS	Dnd41	blood
34	chr19:36426400-36427200	Flanking Active TSS	Osteobl	bone
35	chr19:36426400-36429400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr19:36426600-36426800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
37	chr19:36426600-36426800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr19:36426600-36426800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:36426600-36426800	Flanking Active TSS	H9 Cell Line	embryonic stem cell
40	chr19:36426600-36426800	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr19:36426600-36426800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr19:36426600-36426800	Bivalent Enhancer	Primary B cells from cord blood	blood
43	chr19:36426600-36426800	Flanking Active TSS	Primary T cells from cord blood	blood
44	chr19:36426600-36426800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
45	chr19:36426600-36426800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
46	chr19:36426600-36426800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr19:36426600-36426800	Enhancers	Aorta	Aorta
48	chr19:36426600-36426800	Enhancers	Liver	Liver
49	chr19:36426600-36426800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr19:36426600-36426800	Flanking Active TSS	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links