Variant report

Variant	rs72682904
Chromosome Location	chr8:86057028-86057029
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11261468	0.90[ASN][1000 genomes]
rs2403082	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2403087	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2403088	0.92[ASN][1000 genomes]
rs2403089	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2896452	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2896453	0.84[AMR][1000 genomes]
rs2896454	0.81[ASN][1000 genomes]
rs4150862	0.92[ASN][1000 genomes]
rs4740043	0.93[ASN][1000 genomes]
rs6605609	0.94[ASN][1000 genomes]
rs6605624	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6605625	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6986704	0.96[ASN][1000 genomes]
rs6990256	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7004765	0.81[ASN][1000 genomes]
rs7007304	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7015758	0.81[ASN][1000 genomes]
rs7814435	0.87[ASN][1000 genomes]
rs7818090	0.90[ASN][1000 genomes]
rs7823218	0.81[ASN][1000 genomes]
rs7829144	0.90[ASN][1000 genomes]
rs7838900	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7841142	0.91[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	esv3481417	chr8:85279453-86145229	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv3481418	chr8:85279453-86145229	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv1797206	chr8:86023237-86060072	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	esv1800945	chr8:86030101-86060072	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
5	nsv397288	chr8:86055325-86057070	Weak transcription Strong transcription Enhancers	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs72682904	LRRCC1	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86020000-86057400	Weak transcription	Small Intestine	intestine
2	chr8:86020400-86057400	Weak transcription	Aorta	Aorta
3	chr8:86020400-86062600	Weak transcription	Pancreas	Pancrea
4	chr8:86020600-86058800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr8:86021200-86058800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr8:86021200-86059600	Weak transcription	Fetal Brain Male	brain
7	chr8:86021400-86058400	Weak transcription	Brain Germinal Matrix	brain
8	chr8:86025200-86057400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr8:86028400-86059000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr8:86032800-86057400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr8:86033000-86059800	Weak transcription	Fetal Thymus	thymus
12	chr8:86037000-86061200	Weak transcription	Brain Anterior Caudate	brain
13	chr8:86038000-86057200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr8:86038800-86057400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr8:86039600-86058400	Weak transcription	Esophagus	oesophagus
16	chr8:86040600-86062000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr8:86043000-86058800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr8:86043200-86057200	Weak transcription	Left Ventricle	heart
19	chr8:86044200-86060000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr8:86045600-86057200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr8:86046600-86064800	Weak transcription	Thymus	Thymus
22	chr8:86046600-86065800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr8:86048800-86059000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr8:86049400-86057400	Weak transcription	Fetal Intestine Large	intestine
25	chr8:86049400-86065800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr8:86050800-86061400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr8:86051000-86057200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr8:86051000-86057400	Weak transcription	Adipose Nuclei	Adipose
29	chr8:86051000-86057600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr8:86051000-86059800	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr8:86051200-86057400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr8:86051400-86057800	Weak transcription	Brain Angular Gyrus	brain
33	chr8:86054000-86057600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr8:86054200-86059800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr8:86055000-86057600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr8:86055000-86059800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr8:86055000-86062400	Weak transcription	Dnd41	blood
38	chr8:86055600-86058400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr8:86055800-86057400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr8:86055800-86058200	Weak transcription	Fetal Stomach	stomach
41	chr8:86055800-86058400	Weak transcription	Lung	lung
42	chr8:86055800-86058800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr8:86055800-86059000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr8:86055800-86059200	Weak transcription	Fetal Intestine Small	intestine
45	chr8:86055800-86059600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr8:86056200-86058800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr8:86056400-86058200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr8:86056400-86058800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr8:86056600-86058600	Weak transcription	K562	blood
50	chr8:86057000-86059200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links