Variant report

Variant	rs11970064
Chromosome Location	chr6:53727758-53727759
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53725023..53728197-chr6:53731513..53733872,3	K562	blood:
2	chr6:53664494..53666032-chr6:53727700..53729812,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10456165	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10456673	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap]
rs10456674	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];0.85[TSI][hapmap];0.91[YRI][hapmap]
rs10948782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10948785	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11962552	0.87[CHD][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs12192118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12192689	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12195491	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs12200971	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12201245	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12201913	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202128	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202361	0.93[ASN][1000 genomes]
rs12202762	1.00[CHB][hapmap]
rs12204130	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs12206209	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12211130	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12211680	0.86[JPT][hapmap]
rs12213392	0.86[JPT][hapmap]
rs12213577	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12214863	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13211528	1.00[JPT][hapmap]
rs17748374	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1883632	0.82[LWK][hapmap]
rs35971619	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3935663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4389767	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4639324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55678884	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55931905	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6919015	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7739668	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7745930	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7762326	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]

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
rs11970064	LRRC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53695000-53743200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:53709800-53762200	Weak transcription	Primary B cells from cord blood	blood
3	chr6:53717800-53731800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:53719800-53727800	Enhancers	Brain Hippocampus Middle	brain
5	chr6:53719800-53747800	Weak transcription	Primary T cells from cord blood	blood
6	chr6:53720600-53741400	Weak transcription	Dnd41	blood
7	chr6:53720800-53736600	Weak transcription	Fetal Thymus	thymus
8	chr6:53721600-53728000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:53722000-53748200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:53723000-53728000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:53723000-53728000	Weak transcription	Pancreas	Pancrea
12	chr6:53723000-53728000	Weak transcription	Right Atrium	heart
13	chr6:53723400-53736800	Weak transcription	Stomach Mucosa	stomach
14	chr6:53725000-53728400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr6:53725000-53729400	Enhancers	Brain Germinal Matrix	brain
16	chr6:53725400-53730000	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr6:53725400-53730200	Enhancers	Brain Anterior Caudate	brain
18	chr6:53725400-53730400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:53725600-53728600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:53725800-53728400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:53725800-53730000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr6:53726000-53729000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:53726000-53729000	Enhancers	HMEC	breast
24	chr6:53726200-53729600	Enhancers	Colon Smooth Muscle	Colon
25	chr6:53726400-53729000	Enhancers	Fetal Stomach	stomach
26	chr6:53726400-53730200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:53726600-53727800	Weak transcription	HepG2	liver
28	chr6:53726600-53728200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:53726600-53728400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:53726600-53728400	Enhancers	NH-A	brain
31	chr6:53726600-53728600	Enhancers	Muscle Satellite Cultured Cells	--
32	chr6:53726600-53729400	Enhancers	Fetal Muscle Leg	muscle
33	chr6:53726600-53730200	Enhancers	Rectal Smooth Muscle	rectum
34	chr6:53726600-53730400	Enhancers	Fetal Brain Male	brain
35	chr6:53726800-53728400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:53726800-53728600	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr6:53726800-53729800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr6:53727000-53728800	Weak transcription	Fetal Intestine Small	intestine
39	chr6:53727000-53729200	Enhancers	Fetal Lung	lung
40	chr6:53727200-53728200	Enhancers	Osteobl	bone
41	chr6:53727200-53729000	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr6:53727200-53729400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:53727200-53729400	Enhancers	Fetal Brain Female	brain
44	chr6:53727400-53728000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:53727400-53728200	Enhancers	HUVEC	blood vessel
46	chr6:53727400-53728200	Enhancers	NHDF-Ad	bronchial
47	chr6:53727400-53728400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:53727400-53728400	Flanking Active TSS	HSMMtube	muscle
49	chr6:53727400-53728400	Flanking Active TSS	NHEK	skin
50	chr6:53727400-53729600	Enhancers	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links