Variant report

Variant	rs9446993
Chromosome Location	chr6:74421677-74421678
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs45620342	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72953389	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72953390	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72953401	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9442950	0.82[ASW][hapmap];0.94[LWK][hapmap];0.84[MKK][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes]
rs9442951	0.81[LWK][hapmap]
rs9446990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9446991	0.89[AFR][1000 genomes]
rs9446992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886158	chr6:74126084-74436825	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
2	nsv1027968	chr6:74155378-74521923	Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
3	nsv538305	chr6:74155378-74521923	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	nsv1023250	chr6:74189642-74605976	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS 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	172 gene(s)	inside rSNPs	diseases
5	nsv538306	chr6:74189642-74605976	Strong transcription Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers 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	172 gene(s)	inside rSNPs	diseases
6	nsv1029927	chr6:74300496-74424355	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv463154	chr6:74412048-74775904	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv603695	chr6:74412048-74775904	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	esv3361633	chr6:74420581-74422579	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv2499472	chr6:74420847-74422391	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription	n/a	n/a	inside rSNPs	diseases
11	esv3421625	chr6:74421031-74422079	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
12	esv9431	chr6:74421045-74421783	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
13	esv2379909	chr6:74421070-74421748	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
14	esv3523962	chr6:74421151-74421678	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9446993	CD109	cis	multi-tissue	Pritchard
rs9446993	CD109	cis	lymphoblastoid	seeQTL
rs9446993	SLC17A5	cis	lymphoblastoid	seeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74407200-74421800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr6:74407200-74422400	Weak transcription	Fetal Lung	lung
3	chr6:74407200-74423800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:74407200-74424800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr6:74407400-74423000	Weak transcription	Fetal Muscle Leg	muscle
6	chr6:74407600-74424000	Weak transcription	Right Ventricle	heart
7	chr6:74408000-74446800	Weak transcription	Dnd41	blood
8	chr6:74412800-74423600	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr6:74413600-74422200	Weak transcription	Fetal Heart	heart
10	chr6:74414400-74423000	Weak transcription	Primary T cells from cord blood	blood
11	chr6:74414400-74423200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr6:74414400-74424000	Weak transcription	Placenta	Placenta
13	chr6:74414600-74423000	Weak transcription	Fetal Thymus	thymus
14	chr6:74414800-74422600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:74414800-74423200	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr6:74414800-74474600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr6:74415200-74422200	Weak transcription	Adipose Nuclei	Adipose
18	chr6:74415200-74422400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr6:74415200-74423000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:74415200-74432200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:74417000-74423200	Weak transcription	Lung	lung
22	chr6:74417000-74424000	Weak transcription	Esophagus	oesophagus
23	chr6:74417400-74422200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:74417400-74423400	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr6:74417400-74423800	Weak transcription	Thymus	Thymus
26	chr6:74420200-74422400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:74420200-74422600	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr6:74420200-74422600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:74420400-74423000	Enhancers	Placenta Amnion	Placenta Amnion
30	chr6:74420400-74425200	Enhancers	Primary hematopoietic stem cells	blood
31	chr6:74420600-74422000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:74420600-74422600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:74420600-74423000	Weak transcription	Right Atrium	heart
34	chr6:74420600-74423200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:74420600-74423200	Weak transcription	Osteobl	bone
36	chr6:74420800-74422200	Weak transcription	Colon Smooth Muscle	Colon
37	chr6:74420800-74423000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr6:74420800-74423000	Weak transcription	Brain Substantia Nigra	brain
39	chr6:74421000-74422000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr6:74421000-74422000	Weak transcription	HUVEC	blood vessel
41	chr6:74421000-74422200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr6:74421000-74422200	Weak transcription	NHDF-Ad	bronchial
43	chr6:74421000-74422600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:74421000-74423000	Weak transcription	Left Ventricle	heart
45	chr6:74421000-74423200	Weak transcription	NH-A	brain
46	chr6:74421000-74423400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:74421000-74423600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr6:74421000-74423800	Weak transcription	NHLF	lung
49	chr6:74421000-74424600	Weak transcription	Hela-S3	cervix
50	chr6:74421000-74432200	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links