Variant report

Variant	rs11977915
Chromosome Location	chr7:127283170-127283171
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:127274788..127276346-chr7:127281698..127283951,2	MCF-7	breast:
2	chr7:127282268..127284029-chr7:127290739..127293277,2	MCF-7	breast:
3	chr7:127282540..127285250-chr7:127290240..127292394,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240790	Chromatin interaction
ENSG00000197157	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10215276	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10251423	0.81[ASN][1000 genomes]
rs10255861	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10260037	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1029927	0.81[ASN][1000 genomes]
rs10954163	0.85[ASN][1000 genomes]
rs11521053	0.85[ASN][1000 genomes]
rs11971935	0.85[ASN][1000 genomes]
rs11972774	0.85[ASN][1000 genomes]
rs11976841	0.96[ASN][1000 genomes]
rs11976946	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11977012	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11980318	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531440	0.85[ASN][1000 genomes]
rs12533846	0.85[ASN][1000 genomes]
rs12539728	0.85[ASN][1000 genomes]
rs12540865	0.85[ASN][1000 genomes]
rs13236900	0.81[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13237048	0.85[ASN][1000 genomes]
rs141450	0.85[ASN][1000 genomes]
rs16885524	0.96[ASN][1000 genomes]
rs17151241	0.85[ASN][1000 genomes]
rs17151270	0.85[ASN][1000 genomes]
rs17716738	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17718395	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1860934	0.81[ASN][1000 genomes]
rs1881084	0.90[ASN][1000 genomes]
rs2043982	0.96[ASN][1000 genomes]
rs2119452	0.96[ASN][1000 genomes]
rs2119453	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2141259	0.88[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2402866	0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2402867	0.96[ASN][1000 genomes]
rs325440	0.85[ASN][1000 genomes]
rs325442	0.81[ASN][1000 genomes]
rs325444	0.81[ASN][1000 genomes]
rs325445	0.81[ASN][1000 genomes]
rs325446	0.81[ASN][1000 genomes]
rs325447	0.81[ASN][1000 genomes]
rs325451	0.81[ASN][1000 genomes]
rs327518	0.82[CHB][hapmap];0.87[CHD][hapmap];0.83[ASN][1000 genomes]
rs35121681	0.81[ASN][1000 genomes]
rs35176520	0.85[ASN][1000 genomes]
rs35971861	0.85[ASN][1000 genomes]
rs3779529	0.81[ASN][1000 genomes]
rs3779530	0.81[ASN][1000 genomes]
rs3808092	0.81[ASN][1000 genomes]
rs3808093	0.85[ASN][1000 genomes]
rs3808095	0.85[ASN][1000 genomes]
rs3808097	0.85[ASN][1000 genomes]
rs3808105	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808106	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3808107	0.96[ASN][1000 genomes]
rs3808112	0.96[ASN][1000 genomes]
rs3824000	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3824006	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.80[TSI][hapmap];0.83[ASN][1000 genomes]
rs4728077	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4731376	0.96[ASN][1000 genomes]
rs55694225	0.90[ASN][1000 genomes]
rs56306023	0.93[ASN][1000 genomes]
rs58583807	0.85[ASN][1000 genomes]
rs6961381	0.85[ASN][1000 genomes]
rs6963455	0.85[ASN][1000 genomes]
rs6968199	0.85[ASN][1000 genomes]
rs712716	0.90[JPT][hapmap]
rs717944	0.83[EUR][1000 genomes]
rs73234861	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73234862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73234876	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73234880	0.90[ASN][1000 genomes]
rs73234882	0.90[ASN][1000 genomes]
rs73234897	0.89[ASN][1000 genomes]
rs741599	0.81[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs759843	0.90[ASN][1000 genomes]
rs7786041	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7797663	0.82[ASN][1000 genomes]
rs917832	0.81[ASN][1000 genomes]
rs918793	0.85[ASN][1000 genomes]
rs972088	0.87[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs972089	0.96[ASN][1000 genomes]
rs972090	0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831122	chr7:127143207-127357885	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS 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	37 gene(s)	inside rSNPs	diseases
4	nsv1016143	chr7:127251359-127726762	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS 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 miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1031658	chr7:127266882-127376775	Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11977915	LRRC4	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127276000-127284400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr7:127281400-127284800	Enhancers	Placenta	Placenta
3	chr7:127281600-127283400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:127281800-127283400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr7:127281800-127284000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr7:127281800-127285600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr7:127282200-127283600	Weak transcription	Adipose Nuclei	Adipose
8	chr7:127282200-127283600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr7:127282200-127285800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr7:127282400-127284600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:127282600-127283600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr7:127282600-127283800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr7:127282600-127284400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr7:127282800-127283400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr7:127283000-127291000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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