Variant report

Variant	rs55678884
Chromosome Location	chr6:53694329-53694330
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53668250..53669975-chr6:53693891..53696274,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10948782	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10948785	0.82[AMR][1000 genomes]
rs11970064	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12192118	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12192689	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12195491	1.00[EUR][1000 genomes]
rs12200971	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12201245	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12201913	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12202128	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12202361	0.87[AFR][1000 genomes]
rs12206209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12211130	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12214863	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17748374	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35971619	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3935663	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4389767	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4639324	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55931905	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6919015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7739668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7745930	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7762326	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55678884	LRRC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53676200-53697800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:53680400-53721600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:53680600-53694400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:53684000-53710200	Weak transcription	Primary T cells from cord blood	blood
5	chr6:53684600-53697000	Enhancers	Brain Substantia Nigra	brain
6	chr6:53687600-53702000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:53688000-53694600	Weak transcription	Fetal Muscle Leg	muscle
8	chr6:53689400-53696400	Enhancers	Stomach Mucosa	stomach
9	chr6:53689400-53699400	Enhancers	Fetal Intestine Large	intestine
10	chr6:53689600-53694400	Enhancers	HepG2	liver
11	chr6:53689600-53695400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:53689800-53695000	Enhancers	HMEC	breast
13	chr6:53689800-53695200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:53689800-53697200	Enhancers	Colon Smooth Muscle	Colon
15	chr6:53690000-53695400	Enhancers	Brain Cingulate Gyrus	brain
16	chr6:53690000-53699000	Enhancers	Fetal Intestine Small	intestine
17	chr6:53690200-53695000	Enhancers	Brain Hippocampus Middle	brain
18	chr6:53690200-53695600	Enhancers	NHEK	skin
19	chr6:53690400-53697200	Enhancers	Brain Anterior Caudate	brain
20	chr6:53690800-53695200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:53691200-53697800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:53691400-53695000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:53691400-53697400	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr6:53691800-53695200	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr6:53692000-53694400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr6:53692000-53696000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr6:53692400-53694400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr6:53692400-53695000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:53692400-53695600	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr6:53692400-53696600	Enhancers	Placenta Amnion	Placenta Amnion
31	chr6:53692400-53697800	Weak transcription	Brain Germinal Matrix	brain
32	chr6:53692600-53694600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:53692600-53702600	Weak transcription	Aorta	Aorta
34	chr6:53693000-53695600	Enhancers	Stomach Smooth Muscle	stomach
35	chr6:53693000-53696400	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr6:53693200-53694600	Weak transcription	Hela-S3	cervix
37	chr6:53693200-53695000	Enhancers	H9 Cell Line	embryonic stem cell
38	chr6:53693400-53694400	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr6:53693400-53694400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr6:53693400-53694400	Weak transcription	Esophagus	oesophagus
41	chr6:53693400-53694400	Weak transcription	Gastric	stomach
42	chr6:53693400-53694400	Weak transcription	Ovary	ovary
43	chr6:53693400-53694400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr6:53693400-53694600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:53693400-53694800	Weak transcription	Small Intestine	intestine
46	chr6:53693400-53696800	Weak transcription	HSMMtube	muscle
47	chr6:53693400-53697200	Enhancers	Duodenum Mucosa	Duodenum
48	chr6:53693400-53697800	Weak transcription	Thymus	Thymus
49	chr6:53693400-53700800	Weak transcription	Pancreas	Pancrea
50	chr6:53693400-53701400	Weak transcription	HSMM	muscle

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