Variant report

Variant	rs742108
Chromosome Location	chr6:106582920-106582921
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:106574758..106578826-chr6:106580489..106584982,7	K562	blood:
2	chr6:106576961..106578620-chr6:106582173..106584108,2	MCF-7	breast:
3	chr5:92490041..92490820-chr6:106582809..106583364,2	MCF-7	breast:
4	chr6:105967746..105968312-chr6:106582748..106583466,3	MCF-7	breast:
5	chr6:106342477..106345340-chr6:106581951..106584296,2	MCF-7	breast:
6	chr6:106582685..106586548-chr6:106586639..106589895,5	K562	blood:
7	chr6:106076084..106076590-chr6:106582559..106583472,2	MCF-7	breast:
8	chr6:106582718..106583982-chr6:106633824..106634839,9	MCF-7	breast:
9	chr6:105967746..105968312-chr6:106582748..106583466,2	MCF-7	breast:
10	chr6:106243648..106244392-chr6:106582692..106583246,2	MCF-7	breast:
11	chr6:106582718..106583982-chr6:106633824..106634839,6	MCF-7	breast:
12	chr6:106582911..106584743-chr6:106586663..106589523,3	K562	blood:
13	chr6:106566135..106570137-chr6:106580831..106586138,5	MCF-7	breast:
14	chr6:106567410..106567924-chr6:106582600..106583313,2	MCF-7	breast:
15	chr6:106076089..106076913-chr6:106582564..106583562,2	MCF-7	breast:
16	chr6:106565935..106568775-chr6:106582626..106585270,2	MCF-7	breast:

No data

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1012894	0.88[ASN][1000 genomes]
rs1040893	0.88[ASN][1000 genomes]
rs11152966	0.93[ASN][1000 genomes]
rs11753719	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11753795	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11758079	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11758444	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11758474	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13193993	0.86[ASN][1000 genomes]
rs1883231	0.80[ASN][1000 genomes]
rs34408152	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4134466	0.80[ASN][1000 genomes]
rs6568431	0.94[ASN][1000 genomes]
rs6937876	0.95[ASN][1000 genomes]
rs6939138	0.98[ASN][1000 genomes]
rs7759216	0.93[ASN][1000 genomes]
rs9320151	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9398067	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv1025231	chr6:106451012-106634389	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv830755	chr6:106461705-106624202	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1025900	chr6:106529777-106898421	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1018270	chr6:106531658-106908606	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv538399	chr6:106531658-106908606	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	esv1832544	chr6:106539914-106642993	Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1035110	chr6:106557281-106802212	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv538400	chr6:106557281-106802212	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv1022855	chr6:106570926-106802072	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
11	nsv538401	chr6:106570926-106802072	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Systemic lupus erythematosus	23273568	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs742108	AKD1	cis	parietal	SCAN
rs742108	LIN28B	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106553600-106584000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:106577800-106583000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr6:106578000-106583200	Weak transcription	Fetal Intestine Small	intestine
4	chr6:106578000-106583200	Weak transcription	HSMMtube	muscle
5	chr6:106578200-106583000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:106578400-106585400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:106581400-106589400	Weak transcription	Psoas Muscle	Psoas
8	chr6:106582000-106583000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:106582000-106583400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:106582000-106583400	Enhancers	Esophagus	oesophagus
11	chr6:106582000-106583400	Enhancers	HMEC	breast
12	chr6:106582000-106583600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:106582000-106583600	Enhancers	Placenta	Placenta
14	chr6:106582000-106583600	Enhancers	Placenta Amnion	Placenta Amnion
15	chr6:106582000-106584400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:106582000-106584400	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr6:106582000-106584400	Flanking Active TSS	Hela-S3	cervix
18	chr6:106582200-106583200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr6:106582200-106583200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:106582200-106584400	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr6:106582400-106583000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:106582400-106583000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:106582400-106583200	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr6:106582400-106583600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr6:106582400-106583600	Enhancers	NH-A	brain
26	chr6:106582400-106583800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:106582400-106583800	Flanking Bivalent TSS/Enh	HepG2	liver
28	chr6:106582600-106583000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:106582600-106583000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr6:106582600-106583000	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr6:106582600-106583000	Enhancers	A549	lung
32	chr6:106582600-106583400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:106582600-106583800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:106582600-106584400	Enhancers	K562	blood
35	chr6:106582800-106583000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:106582800-106583200	Flanking Active TSS	NHDF-Ad	bronchial
37	chr6:106582800-106583200	Enhancers	NHLF	lung
38	chr6:106582800-106583400	Enhancers	NHEK	skin
39	chr6:106582800-106583600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr6:106582800-106583600	Flanking Active TSS	Osteobl	bone
41	chr6:106582800-106583800	Enhancers	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links