Variant report

Variant	rs3813505
Chromosome Location	chr7:56132122-56132123
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:74033538..74034177-chr7:56131927..56132900,2	NB4	blood:
2	chr7:56117123..56123487-chr7:56128716..56133468,11	MCF-7	breast:
3	chr7:56018165..56022272-chr7:56129856..56132253,4	K562	blood:
4	chr7:56131320..56133312-chr7:56141582..56144695,3	MCF-7	breast:
5	chr7:56126631..56129395-chr7:56129953..56133299,4	MCF-7	breast:
6	chr7:56124986..56128195-chr7:56129879..56132286,4	MCF-7	breast:
7	chr7:56018384..56020889-chr7:56129856..56132224,2	K562	blood:
8	chr7:56031242..56032808-chr7:56131882..56133699,2	K562	blood:
9	chr11:64901616..64902438-chr7:56131650..56132477,2	Hela-S3	cervix:
10	chr7:56132043..56135542-chr7:56146792..56149237,3	K562	blood:
11	chr7:56130207..56133425-chr7:56142360..56145052,4	K562	blood:
12	chr7:56132081..56135205-chr7:56137628..56140599,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000206603	Chromatin interaction
ENSG00000168209	Chromatin interaction
ENSG00000146731	Chromatin interaction
ENSG00000162298	Chromatin interaction
ENSG00000239789	Chromatin interaction
ENSG00000146729	Chromatin interaction
ENSG00000207168	Chromatin interaction
ENSG00000129103	Chromatin interaction
ENSG00000146733	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10265826	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10274148	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10800	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12154781	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12155441	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12536548	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12537948	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12668193	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12668532	0.95[CEU][hapmap]
rs12671494	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12673255	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13438048	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2014042	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242509	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2270244	0.84[CEU][hapmap]
rs28438587	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28558245	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3778867	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4345511	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4424212	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4427122	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4585698	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55940597	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58251663	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59723101	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6947671	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6955639	0.95[CEU][hapmap]
rs6960348	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6970842	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6971804	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73140779	0.95[AFR][1000 genomes]
rs73140793	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73140794	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs766334	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7778601	0.95[CEU][hapmap]
rs7793536	1.00[CEU][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7793614	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers 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	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription 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	82 gene(s)	inside rSNPs	diseases
4	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
6	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
8	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription 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	68 gene(s)	inside rSNPs	diseases
9	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3813505	SUMF2	cis	lung	GTEx
rs3813505	SUMF2	cis	Whole Blood	GTEx
rs3813505	SUMF2	cis	Esophagus Muscularis	GTEx
rs3813505	SUMF2	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56131400-56133000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr7:56131400-56133200	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr7:56131400-56133200	Active TSS	Brain Anterior Caudate	brain
4	chr7:56131400-56133200	Active TSS	Brain Germinal Matrix	brain
5	chr7:56131400-56133200	Active TSS	Colon Smooth Muscle	Colon
6	chr7:56131400-56133200	Active TSS	Thymus	Thymus
7	chr7:56131600-56132200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr7:56131600-56132400	Active TSS	Primary T killer memory cells from peripheral blood	blood
9	chr7:56131600-56132400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
10	chr7:56131600-56132800	Active TSS	Primary monocytes fromperipheralblood	blood
11	chr7:56131600-56133000	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr7:56131600-56133000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr7:56131600-56133000	Active TSS	Brain Hippocampus Middle	brain
14	chr7:56131600-56133000	Active TSS	Fetal Intestine Small	intestine
15	chr7:56131600-56133200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr7:56131600-56133200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr7:56131600-56133200	Active TSS	H9 Cell Line	embryonic stem cell
18	chr7:56131600-56133200	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr7:56131600-56133200	Active TSS	Colonic Mucosa	Colon
20	chr7:56131600-56133200	Active TSS	Esophagus	oesophagus
21	chr7:56131600-56133200	Active TSS	Fetal Lung	lung
22	chr7:56131600-56133200	Active TSS	Fetal Muscle Trunk	muscle
23	chr7:56131600-56133200	Active TSS	Left Ventricle	heart
24	chr7:56131600-56133200	Active TSS	Ovary	ovary
25	chr7:56131600-56133200	Active TSS	Psoas Muscle	Psoas
26	chr7:56131600-56133200	Active TSS	Right Ventricle	heart
27	chr7:56131600-56133600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr7:56131600-56133800	Active TSS	Placenta	Placenta
29	chr7:56131800-56132200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
30	chr7:56131800-56132200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr7:56131800-56132200	Bivalent/Poised TSS	Aorta	Aorta
32	chr7:56131800-56132200	Transcr. at gene 5' and 3'	Gastric	stomach
33	chr7:56131800-56132200	Transcr. at gene 5' and 3'	Right Atrium	heart
34	chr7:56131800-56132400	Active TSS	Stomach Mucosa	stomach
35	chr7:56131800-56132400	Active TSS	Spleen	Spleen
36	chr7:56131800-56132600	Active TSS	Lung	lung
37	chr7:56131800-56132600	Active TSS	Small Intestine	intestine
38	chr7:56131800-56132800	Active TSS	Primary B cells from peripheral blood	blood
39	chr7:56131800-56132800	Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr7:56131800-56132800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr7:56131800-56132800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr7:56131800-56132800	Active TSS	Placenta Amnion	Placenta Amnion
43	chr7:56131800-56132800	Active TSS	Sigmoid Colon	Sigmoid Colon
44	chr7:56131800-56133000	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr7:56131800-56133000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr7:56131800-56133000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr7:56131800-56133000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr7:56131800-56133000	Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr7:56131800-56133000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr7:56131800-56133000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links