Variant report

Variant	rs11882386
Chromosome Location	chr19:36428708-36428709
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:36427493..36430345-chr19:36435418..36438366,3	MCF-7	breast:
2	chr19:36393311..36395845-chr19:36427548..36429396,2	MCF-7	breast:
3	chr19:36427517..36430098-chr19:36486010..36488671,2	K562	blood:
4	chr19:36426653..36429173-chr19:36484778..36487537,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205138	Chromatin interaction
ENSG00000126264	Chromatin interaction
ENSG00000267786	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10221461	0.85[ASN][1000 genomes]
rs10221486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1057265	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11878444	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11878880	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11879537	0.87[AMR][1000 genomes];0.86[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	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11883234	0.91[ASN][1000 genomes]
rs13382036	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2242590	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293756	0.93[ASN][1000 genomes]
rs230260	0.81[EUR][1000 genomes]
rs34933126	0.90[EUR][1000 genomes]
rs55686886	0.93[ASN][1000 genomes]
rs56042927	0.93[ASN][1000 genomes]
rs56132631	0.83[ASN][1000 genomes]
rs56132838	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56187901	0.93[ASN][1000 genomes]
rs56230692	0.93[ASN][1000 genomes]
rs56744930	0.90[EUR][1000 genomes]
rs56922307	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57068163	0.90[EUR][1000 genomes]
rs57094555	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57516855	0.85[EUR][1000 genomes]
rs57785375	0.93[ASN][1000 genomes]
rs57962062	0.86[EUR][1000 genomes]
rs58161969	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58291714	0.81[EUR][1000 genomes]
rs58456578	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58504183	0.95[EUR][1000 genomes]
rs58551711	0.95[EUR][1000 genomes]
rs58768499	0.90[ASN][1000 genomes]
rs58976020	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59150589	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59151712	0.93[ASN][1000 genomes]
rs59399698	0.85[EUR][1000 genomes]
rs59416903	0.86[EUR][1000 genomes]
rs59478831	0.81[EUR][1000 genomes]
rs59534183	0.85[EUR][1000 genomes]
rs60073802	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60268250	0.81[EUR][1000 genomes]
rs60276253	0.93[ASN][1000 genomes]
rs60500471	0.93[ASN][1000 genomes]
rs60576074	0.81[EUR][1000 genomes]
rs60869994	0.81[EUR][1000 genomes]
rs60892678	0.93[ASN][1000 genomes]
rs60935148	0.95[EUR][1000 genomes]
rs61510077	0.88[ASN][1000 genomes]
rs61660311	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61672461	0.90[EUR][1000 genomes]
rs7245383	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs7246259	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7247000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[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];0.82[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]
rs7252053	0.85[ASN][1000 genomes]
rs7252526	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7252572	0.90[ASN][1000 genomes]
rs7252693	0.93[ASN][1000 genomes]
rs7252839	0.93[ASN][1000 genomes]
rs7253086	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7254298	0.93[ASN][1000 genomes]
rs7254335	0.86[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	0.90[EUR][1000 genomes]
rs7256433	0.95[EUR][1000 genomes]
rs7256952	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[ASN][1000 genomes]
rs7257789	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]
rs7257911	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7258914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7259892	0.93[ASN][1000 genomes]
rs7260613	0.85[GIH][hapmap];0.81[EUR][1000 genomes]
rs73590883	0.81[EUR][1000 genomes]
rs73599539	0.90[EUR][1000 genomes]
rs73599540	0.90[EUR][1000 genomes]
rs73599546	0.90[EUR][1000 genomes]
rs73599554	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73599561	0.90[EUR][1000 genomes]
rs73599565	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73599577	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73599586	0.90[EUR][1000 genomes]
rs73599600	0.95[EUR][1000 genomes]
rs73599602	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73928364	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73928368	0.93[ASN][1000 genomes]
rs73928369	0.93[ASN][1000 genomes]
rs8110868	0.90[EUR][1000 genomes]
rs909135	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs909136	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9749492	0.81[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11882386	LRFN3	cis	lymphoblastoid	seeQTL
rs11882386	LRFN3	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36426400-36429400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr19:36426600-36429400	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr19:36426800-36428800	Active TSS	H9 Cell Line	embryonic stem cell
4	chr19:36427000-36428800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:36427000-36429000	Active TSS	Fetal Kidney	kidney
6	chr19:36427000-36429600	Active TSS	NHLF	lung
7	chr19:36427000-36429800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:36427000-36429800	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr19:36427200-36429000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr19:36427200-36429000	Active TSS	HSMM	muscle
11	chr19:36427200-36429600	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr19:36427200-36429600	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr19:36427600-36428800	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr19:36427600-36428800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
15	chr19:36427600-36428800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr19:36427600-36428800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr19:36427600-36428800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
18	chr19:36427600-36428800	Flanking Active TSS	Thymus	Thymus
19	chr19:36427600-36428800	Flanking Active TSS	HUVEC	blood vessel
20	chr19:36427600-36429000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr19:36427600-36429000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
22	chr19:36427600-36429000	Flanking Active TSS	Colonic Mucosa	Colon
23	chr19:36427600-36429000	Flanking Active TSS	NH-A	brain
24	chr19:36427600-36429000	Flanking Active TSS	Osteobl	bone
25	chr19:36427600-36429200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr19:36427600-36429200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr19:36427600-36429400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
28	chr19:36427600-36429400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr19:36427600-36429600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr19:36427600-36429600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr19:36427600-36429600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr19:36427600-36429600	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr19:36427600-36429600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr19:36427600-36429800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr19:36427600-36429800	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr19:36427600-36429800	Flanking Active TSS	Dnd41	blood
37	chr19:36427800-36428800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:36427800-36428800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr19:36427800-36428800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
40	chr19:36427800-36428800	Enhancers	Spleen	Spleen
41	chr19:36427800-36429000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr19:36427800-36429000	Flanking Active TSS	Brain Substantia Nigra	brain
43	chr19:36427800-36429000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
44	chr19:36427800-36429000	Flanking Active TSS	Right Ventricle	heart
45	chr19:36427800-36429000	Flanking Active TSS	A549	lung
46	chr19:36427800-36429000	Flanking Active TSS	NHEK	skin
47	chr19:36427800-36429200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr19:36427800-36429200	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr19:36427800-36429400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr19:36427800-36429400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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