Variant report

Variant	rs7256952
Chromosome Location	chr19:36436696-36436697
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	POLR2A	chr19:36436620-36436748	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36434768..36437556-chr19:36487858..36489977,3	MCF-7	breast:
2	chr19:36427493..36430345-chr19:36435418..36438366,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267786	TF binding region
ENSG00000126243	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10221461	0.92[ASN][1000 genomes]
rs10221486	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10402798	1.00[TSI][hapmap]
rs1057265	0.91[ASN][1000 genomes]
rs11878444	0.93[ASN][1000 genomes]
rs11878547	1.00[CEU][hapmap]
rs11878880	0.86[ASN][1000 genomes]
rs11879537	0.86[ASN][1000 genomes]
rs11880835	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11880859	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11881157	0.91[ASN][1000 genomes]
rs11882386	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[ASN][1000 genomes]
rs11883234	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13382036	0.91[ASN][1000 genomes]
rs16960862	1.00[CEU][hapmap]
rs1802029	1.00[CEU][hapmap]
rs2242590	0.93[ASN][1000 genomes]
rs2293756	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3761086	1.00[CEU][hapmap]
rs55686886	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56042927	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56132631	0.90[ASN][1000 genomes]
rs56132838	0.87[ASN][1000 genomes]
rs56187901	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56230692	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56922307	0.91[ASN][1000 genomes]
rs57094555	0.91[ASN][1000 genomes]
rs57785375	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58161969	0.91[ASN][1000 genomes]
rs58456578	0.91[ASN][1000 genomes]
rs58768499	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58976020	0.93[ASN][1000 genomes]
rs59150589	0.91[ASN][1000 genomes]
rs59151712	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60073802	0.91[ASN][1000 genomes]
rs60276253	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60500471	1.00[ASN][1000 genomes]
rs60892678	1.00[ASN][1000 genomes]
rs61510077	0.95[ASN][1000 genomes]
rs61660311	0.83[ASN][1000 genomes]
rs7245383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246259	0.93[ASN][1000 genomes]
rs7246541	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[ASN][1000 genomes]
rs7247000	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7247246	1.00[JPT][hapmap]
rs7247769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248253	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7248265	1.00[ASN][1000 genomes]
rs7249502	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249567	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.84[ASN][1000 genomes]
rs7251380	1.00[ASN][1000 genomes]
rs7251422	0.92[ASN][1000 genomes]
rs7252053	0.92[ASN][1000 genomes]
rs7252526	0.86[ASN][1000 genomes]
rs7252572	0.83[ASN][1000 genomes]
rs7252693	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7252839	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254113	1.00[CEU][hapmap]
rs7254298	1.00[ASN][1000 genomes]
rs7254905	1.00[ASN][1000 genomes]
rs7254994	1.00[ASN][1000 genomes]
rs7255824	1.00[ASN][1000 genomes]
rs7257789	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7257911	0.89[ASN][1000 genomes]
rs7258914	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7259892	1.00[ASN][1000 genomes]
rs73599554	0.86[ASN][1000 genomes]
rs73599565	0.86[ASN][1000 genomes]
rs73599577	0.93[ASN][1000 genomes]
rs73599602	0.93[ASN][1000 genomes]
rs73928364	0.86[ASN][1000 genomes]
rs73928368	1.00[ASN][1000 genomes]
rs73928369	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8101472	1.00[CEU][hapmap]
rs8103718	1.00[CEU][hapmap]
rs8106480	1.00[CEU][hapmap]
rs8106495	1.00[CEU][hapmap]
rs8110231	1.00[CEU][hapmap]
rs8113524	1.00[CEU][hapmap]
rs909135	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[ASN][1000 genomes]
rs909136	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	esv3426319	chr19:36434362-36436860	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7256952	LRFN3	cis	multi-tissue	Pritchard

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36428800-36437000	Weak transcription	HSMMtube	muscle
2	chr19:36429000-36438000	Weak transcription	Osteobl	bone
3	chr19:36429200-36437000	Weak transcription	Psoas Muscle	Psoas
4	chr19:36429200-36438600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:36429400-36438000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:36429400-36438000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr19:36429400-36440000	Weak transcription	A549	lung
8	chr19:36429600-36438000	Strong transcription	Fetal Stomach	stomach
9	chr19:36429600-36439600	Weak transcription	Fetal Lung	lung
10	chr19:36429600-36444200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr19:36429800-36438000	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr19:36429800-36438000	Weak transcription	Colon Smooth Muscle	Colon
13	chr19:36429800-36438400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr19:36429800-36438600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr19:36429800-36438600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr19:36429800-36441000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr19:36430000-36450000	Weak transcription	Right Atrium	heart
18	chr19:36430200-36436800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr19:36430800-36438400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr19:36431000-36438000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr19:36431800-36437600	Weak transcription	Left Ventricle	heart
22	chr19:36431800-36437800	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr19:36431800-36437800	Weak transcription	Colonic Mucosa	Colon
24	chr19:36431800-36438000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr19:36431800-36438000	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr19:36431800-36438000	Weak transcription	NHLF	lung
27	chr19:36431800-36438200	Weak transcription	Brain Angular Gyrus	brain
28	chr19:36431800-36438600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr19:36431800-36440200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr19:36431800-36440400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr19:36431800-36442800	Weak transcription	Thymus	Thymus
32	chr19:36431800-36443000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr19:36432000-36438000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr19:36432400-36437600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr19:36432400-36440200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr19:36433000-36436800	Strong transcription	Brain Cingulate Gyrus	brain
37	chr19:36433000-36436800	Strong transcription	Stomach Smooth Muscle	stomach
38	chr19:36433200-36437400	Strong transcription	Fetal Intestine Small	intestine
39	chr19:36433400-36438000	Weak transcription	Brain Substantia Nigra	brain
40	chr19:36433600-36438000	Weak transcription	Adipose Nuclei	Adipose
41	chr19:36433600-36438200	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr19:36433600-36438400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr19:36433600-36439200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr19:36433600-36444200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr19:36433800-36437800	Weak transcription	Liver	Liver
46	chr19:36434600-36437800	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr19:36435200-36436800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr19:36435200-36437800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr19:36435200-36440000	Weak transcription	Fetal Muscle Leg	muscle
50	chr19:36435400-36437400	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links