Variant report

Variant	rs12208080
Chromosome Location	chr6:53766751-53766752
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:53762030..53763793-chr6:53766610..53769238,2	K562	blood:
2	chr6:53762293..53765107-chr6:53765198..53769238,3	K562	blood:
3	chr6:53765189..53768016-chr6:53774461..53775969,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1076701	0.82[JPT][hapmap]
rs11758405	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12663216	0.89[CHB][hapmap]
rs1883632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3003492	0.93[CHB][hapmap]
rs3003498	0.89[CHB][hapmap]
rs35236104	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35682826	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4486000	0.89[CHB][hapmap]
rs6905563	0.82[CHB][hapmap]
rs6906326	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12208080	LRRC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53737800-53768400	Weak transcription	Esophagus	oesophagus
2	chr6:53739000-53767800	Weak transcription	Ovary	ovary
3	chr6:53739000-53771800	Weak transcription	Pancreas	Pancrea
4	chr6:53746800-53768400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr6:53747600-53767800	Weak transcription	Small Intestine	intestine
6	chr6:53752400-53771000	Weak transcription	Gastric	stomach
7	chr6:53752400-53771800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:53752800-53782000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr6:53754800-53775600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr6:53754800-53779800	Weak transcription	NHLF	lung
11	chr6:53755000-53779800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:53756000-53781800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:53757800-53767400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:53757800-53768000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr6:53758000-53775600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:53759200-53767600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr6:53759200-53767600	Weak transcription	Lung	lung
18	chr6:53759200-53767800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:53759200-53769400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr6:53759200-53770800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr6:53759200-53787600	Weak transcription	Spleen	Spleen
22	chr6:53759200-53794400	Weak transcription	Right Ventricle	heart
23	chr6:53759400-53767600	Weak transcription	Thymus	Thymus
24	chr6:53759400-53768200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr6:53759400-53770000	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr6:53759400-53771800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr6:53759400-53786400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr6:53759600-53767000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr6:53759600-53789800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:53760400-53789400	Weak transcription	Stomach Mucosa	stomach
31	chr6:53760400-53791200	Weak transcription	Hela-S3	cervix
32	chr6:53760600-53773000	Strong transcription	Dnd41	blood
33	chr6:53760600-53778800	Weak transcription	Fetal Muscle Leg	muscle
34	chr6:53760600-53793600	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr6:53760800-53771800	Weak transcription	Brain Angular Gyrus	brain
36	chr6:53761000-53768200	Weak transcription	Aorta	Aorta
37	chr6:53761000-53770800	Weak transcription	Brain Substantia Nigra	brain
38	chr6:53761000-53771200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr6:53761000-53771600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr6:53761000-53771800	Weak transcription	Brain Anterior Caudate	brain
41	chr6:53761000-53782000	Weak transcription	Fetal Kidney	kidney
42	chr6:53761000-53782800	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr6:53761000-53785400	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr6:53761400-53771800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr6:53761400-53776400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr6:53761400-53787400	Weak transcription	HMEC	breast
47	chr6:53761400-53791200	Weak transcription	Colon Smooth Muscle	Colon
48	chr6:53761600-53767600	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr6:53761600-53771000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:53761600-53790800	Weak transcription	Fetal Heart	heart

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