Variant report

Variant	rs2814948
Chromosome Location	chr6:34653413-34653414
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	chr6:34651137..34654420-chr6:34758676..34761167,3	MCF-7	breast:
2	chr6:34653279..34655876-chr6:34663256..34664778,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPDEF-1	chr6:34653134-34653419	NONHSAT112142

Variant related genes	Relation type
ENSG00000065060	Chromatin interaction
ENSG00000196821	Chromatin interaction
ENSG00000272288	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11752260	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11756392	0.83[EUR][1000 genomes]
rs11759235	0.85[EUR][1000 genomes]
rs1555773	0.85[EUR][1000 genomes]
rs2092344	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2395607	0.82[EUR][1000 genomes]
rs2492859	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2492863	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2744937	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2744938	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2744939	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2744942	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2744947	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2744954	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2744955	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2744956	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2744964	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2744965	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2744971	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2744972	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2744977	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2764203	0.88[EUR][1000 genomes]
rs2764204	0.88[EUR][1000 genomes]
rs2764205	0.89[EUR][1000 genomes]
rs2814943	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2814944	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2814960	0.85[EUR][1000 genomes]
rs2814962	0.85[EUR][1000 genomes]
rs2814973	0.87[EUR][1000 genomes]
rs2814977	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2814983	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2814985	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2814986	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2814993	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2814994	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2814996	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2815005	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28567450	0.89[EUR][1000 genomes]
rs3800457	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56693020	0.85[EUR][1000 genomes]
rs56930444	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59142559	0.85[EUR][1000 genomes]
rs60643641	0.81[EUR][1000 genomes]
rs61431557	0.80[EUR][1000 genomes]
rs6457790	0.89[EUR][1000 genomes]
rs6911549	0.85[EUR][1000 genomes]
rs6936177	0.85[EUR][1000 genomes]
rs6938239	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73419607	0.83[EUR][1000 genomes]
rs73419621	0.81[EUR][1000 genomes]
rs7755822	0.85[EUR][1000 genomes]
rs7762485	0.81[EUR][1000 genomes]
rs9296130	0.81[EUR][1000 genomes]
rs9462012	0.86[EUR][1000 genomes]
rs9462014	0.85[EUR][1000 genomes]
rs9462016	0.89[EUR][1000 genomes]
rs9462025	0.85[EUR][1000 genomes]
rs9469860	0.91[EUR][1000 genomes]
rs9469864	0.89[EUR][1000 genomes]
rs9469890	0.85[EUR][1000 genomes]
rs9469895	0.85[EUR][1000 genomes]
rs9469897	0.81[EUR][1000 genomes]
rs9469907	0.82[EUR][1000 genomes]
rs9654581	0.83[EUR][1000 genomes]
rs9688715	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv2758046	chr6:34382492-34714677	Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	esv2759418	chr6:34382492-34714677	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv885785	chr6:34404636-34874002	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv1033583	chr6:34471572-34828372	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv885793	chr6:34520267-34886436	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv830640	chr6:34542489-34714677	Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv885794	chr6:34561585-34673149	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	nsv1032557	chr6:34565802-34802008	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv538196	chr6:34565802-34802008	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
12	esv2763967	chr6:34566255-34925463	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
13	nsv1020710	chr6:34607214-34890143	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2814948	C6orf107	Cis_1M	lymphoblastoid	RTeQTL
rs2814948	C6orf106	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34626000-34662000	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr6:34626800-34662400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr6:34632800-34655200	Weak transcription	Fetal Stomach	stomach
4	chr6:34633000-34662800	Weak transcription	Aorta	Aorta
5	chr6:34634800-34663200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:34636400-34662200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:34639800-34662800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:34639800-34662800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr6:34640200-34656600	Weak transcription	Spleen	Spleen
10	chr6:34640800-34655800	Weak transcription	Fetal Muscle Leg	muscle
11	chr6:34641400-34662800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:34641600-34654800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:34641600-34654800	Weak transcription	Dnd41	blood
14	chr6:34641600-34655400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:34641800-34656400	Weak transcription	Left Ventricle	heart
16	chr6:34641800-34661200	Weak transcription	Brain Hippocampus Middle	brain
17	chr6:34641800-34663200	Weak transcription	Gastric	stomach
18	chr6:34642200-34656000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:34642200-34663000	Weak transcription	Thymus	Thymus
20	chr6:34643000-34655400	Weak transcription	Fetal Thymus	thymus
21	chr6:34643000-34655800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr6:34643000-34655800	Weak transcription	Lung	lung
23	chr6:34643000-34656400	Weak transcription	Pancreas	Pancrea
24	chr6:34643000-34661200	Weak transcription	Right Atrium	heart
25	chr6:34643000-34662800	Weak transcription	Stomach Mucosa	stomach
26	chr6:34647800-34660800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr6:34647800-34661000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr6:34647800-34662000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:34647800-34662200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:34647800-34662400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr6:34647800-34662600	Weak transcription	Ovary	ovary
32	chr6:34647800-34662800	Weak transcription	Brain Substantia Nigra	brain
33	chr6:34647800-34662800	Weak transcription	HSMMtube	muscle
34	chr6:34648000-34662600	Weak transcription	Right Ventricle	heart
35	chr6:34648000-34662800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr6:34648400-34655800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:34648400-34662000	Weak transcription	Brain Anterior Caudate	brain
38	chr6:34649200-34660200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr6:34649200-34660400	Weak transcription	Primary T cells from cord blood	blood
40	chr6:34649200-34662200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr6:34649200-34662600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr6:34649400-34654400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:34649400-34655600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr6:34649400-34655600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr6:34649400-34655800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:34649400-34656000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:34649400-34656600	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr6:34649400-34656600	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr6:34649400-34660200	Weak transcription	NHEK	skin
50	chr6:34649400-34661600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links