Variant report

Variant	rs7762326
Chromosome Location	chr6:53680002-53680003
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	chr6:53678291..53681070-chr6:53681168..53683223,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10456165	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10456673	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10456674	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10948782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10948785	0.86[AMR][1000 genomes]
rs11968082	0.81[ASN][1000 genomes]
rs11970064	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12192118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12192689	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12195491	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes]
rs12200971	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12201245	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12201913	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12202128	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12202762	1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12204130	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12206209	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12211130	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12211417	0.92[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12211478	0.81[ASN][1000 genomes]
rs12211680	0.86[JPT][hapmap]
rs12213392	0.86[JPT][hapmap]
rs12213577	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12214863	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12216441	0.81[ASN][1000 genomes]
rs13205690	0.81[ASN][1000 genomes]
rs13211528	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17748374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34113003	0.82[AFR][1000 genomes]
rs35078422	0.81[ASN][1000 genomes]
rs35143842	0.81[ASN][1000 genomes]
rs35971619	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3935663	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4373362	0.81[ASN][1000 genomes]
rs4389767	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4639324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55678884	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55931905	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6919015	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72941941	0.81[ASN][1000 genomes]
rs7739668	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7745930	0.98[AMR][1000 genomes];0.96[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
rs7762326	LRRC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53661400-53688200	Weak transcription	Right Ventricle	heart
2	chr6:53668200-53680200	Weak transcription	Fetal Stomach	stomach
3	chr6:53668800-53683800	Weak transcription	Ovary	ovary
4	chr6:53670200-53686400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:53670800-53693200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:53671000-53680200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:53671000-53683600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:53671200-53680400	Weak transcription	Fetal Brain Female	brain
9	chr6:53673400-53687200	Weak transcription	Fetal Muscle Leg	muscle
10	chr6:53673600-53682800	Weak transcription	Dnd41	blood
11	chr6:53674800-53680400	Enhancers	Fetal Intestine Small	intestine
12	chr6:53675000-53681200	Weak transcription	Fetal Brain Male	brain
13	chr6:53675400-53680200	Enhancers	Stomach Mucosa	stomach
14	chr6:53675400-53680400	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr6:53676200-53683600	Weak transcription	Left Ventricle	heart
16	chr6:53676200-53697800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:53676800-53680400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr6:53676800-53680400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:53676800-53686800	Weak transcription	Right Atrium	heart
20	chr6:53676800-53687200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr6:53677400-53680600	Enhancers	Fetal Intestine Large	intestine
22	chr6:53677600-53680400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:53677600-53680600	Enhancers	Brain Anterior Caudate	brain
24	chr6:53677600-53680600	Enhancers	Small Intestine	intestine
25	chr6:53677600-53680600	Enhancers	HepG2	liver
26	chr6:53677800-53681600	Enhancers	Brain Hippocampus Middle	brain
27	chr6:53678000-53683600	Weak transcription	HMEC	breast
28	chr6:53678200-53680200	Weak transcription	NHEK	skin
29	chr6:53678400-53680200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:53678400-53680600	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr6:53678400-53681200	Enhancers	Brain Substantia Nigra	brain
32	chr6:53678400-53683600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:53678600-53680200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:53678600-53680200	Weak transcription	Lung	lung
35	chr6:53678600-53680600	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr6:53678600-53680600	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr6:53678600-53681400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:53678600-53692200	Weak transcription	Esophagus	oesophagus
39	chr6:53678800-53680400	Weak transcription	HSMMtube	muscle
40	chr6:53678800-53680600	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr6:53678800-53680600	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr6:53679000-53680200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr6:53679000-53680400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr6:53679200-53680200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:53679200-53680400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr6:53679200-53680400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:53679400-53680600	Enhancers	Aorta	Aorta
48	chr6:53679400-53682000	Enhancers	Colon Smooth Muscle	Colon
49	chr6:53679400-53683200	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr6:53679400-53685200	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links