Variant report

Variant	rs60467893
Chromosome Location	chr6:53672749-53672750
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:53668227..53671026-chr6:53671811..53674151,2	MCF-7	breast:
2	chr6:53672081..53674984-chr6:53705343..53707160,2	MCF-7	breast:
3	chr6:53663341..53666059-chr6:53671400..53673766,2	MCF-7	breast:
4	chr6:53671854..53673444-chr6:53682878..53685695,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11759220	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12661475	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12661938	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12663216	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3001004	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3001005	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3001006	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3001007	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3001008	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3003488	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3003490	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3003492	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3003494	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3003498	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3813850	0.82[EUR][1000 genomes]
rs4254992	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4486000	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4540263	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4582388	0.89[ASN][1000 genomes]
rs4618525	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4640878	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4645422	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4715427	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4715428	0.80[ASN][1000 genomes]
rs4715429	0.88[ASN][1000 genomes]
rs62397076	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62397090	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6458956	0.82[EUR][1000 genomes]
rs6905323	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6905563	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6909040	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6909094	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6925391	0.88[ASN][1000 genomes]
rs7750173	0.92[EUR][1000 genomes]
rs9296720	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9463983	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9463988	0.88[ASN][1000 genomes]
rs9474661	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9474665	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv3474747	chr6:53648744-53677210	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3474748	chr6:53648758-53677207	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60467893	LRRC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53661400-53675600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr6:53661400-53688200	Weak transcription	Right Ventricle	heart
3	chr6:53662600-53677600	Weak transcription	Small Intestine	intestine
4	chr6:53662800-53675400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr6:53664800-53673400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:53665000-53674800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:53665000-53675600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:53667600-53678400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:53667800-53673600	Enhancers	Brain Substantia Nigra	brain
10	chr6:53668200-53680200	Weak transcription	Fetal Stomach	stomach
11	chr6:53668600-53674400	Enhancers	Brain Hippocampus Middle	brain
12	chr6:53668800-53674400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:53668800-53674800	Weak transcription	Lung	lung
14	chr6:53668800-53676000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:53668800-53676000	Weak transcription	HUVEC	blood vessel
16	chr6:53668800-53680000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr6:53668800-53683800	Weak transcription	Ovary	ovary
18	chr6:53669600-53674000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:53669800-53676800	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr6:53670200-53672800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:53670200-53675600	Weak transcription	Left Ventricle	heart
22	chr6:53670200-53678000	Weak transcription	Aorta	Aorta
23	chr6:53670200-53686400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:53670400-53675600	Weak transcription	Fetal Intestine Large	intestine
25	chr6:53670400-53676000	Weak transcription	Colon Smooth Muscle	Colon
26	chr6:53670600-53673200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr6:53670800-53672800	Weak transcription	Dnd41	blood
28	chr6:53670800-53673200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:53670800-53674600	Weak transcription	NHEK	skin
30	chr6:53670800-53675000	Weak transcription	HMEC	breast
31	chr6:53670800-53676000	Weak transcription	Right Atrium	heart
32	chr6:53670800-53680000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr6:53670800-53693200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr6:53671000-53673000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:53671000-53675600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr6:53671000-53675600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr6:53671000-53675600	Weak transcription	Esophagus	oesophagus
38	chr6:53671000-53676400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr6:53671000-53680200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr6:53671000-53683600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr6:53671200-53675600	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr6:53671200-53675800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr6:53671200-53680400	Weak transcription	Fetal Brain Female	brain
44	chr6:53671400-53673200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr6:53671400-53675600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:53671400-53675600	Weak transcription	Primary T cells from cord blood	blood
47	chr6:53671400-53675600	Weak transcription	Pancreas	Pancrea
48	chr6:53671400-53675800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr6:53671400-53676000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:53671400-53676000	Weak transcription	Brain Anterior Caudate	brain

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