Variant report

Variant	rs319683
Chromosome Location	chr3:47933338-47933339
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:47932949-47934284	H1-neurons	neurons:	n/a	n/a
2	REST	chr3:47930541-47934522	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
MAP4	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1060407	0.83[YRI][hapmap]
rs11707679	0.83[YRI][hapmap]
rs11712464	0.83[YRI][hapmap]
rs12635438	0.83[YRI][hapmap]
rs1486916	0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2351249	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2593817	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs319693	0.83[YRI][hapmap]
rs34675858	0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs3731539	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3731547	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4476528	1.00[AMR][1000 genomes]
rs4858863	0.83[YRI][hapmap]
rs55736379	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55808934	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442092	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442103	1.00[EUR][1000 genomes]
rs6442104	1.00[AMR][1000 genomes]
rs6773945	1.00[AMR][1000 genomes]
rs6776963	0.83[YRI][hapmap]
rs6803741	0.83[YRI][hapmap]
rs7372108	1.00[AMR][1000 genomes]
rs73831515	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831540	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831544	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7629850	0.83[YRI][hapmap]
rs9863220	1.00[AMR][1000 genomes];1.00[EUR][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	nsv1006560	chr3:47867461-48037031	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
2	nsv1011662	chr3:47891634-48019462	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv536561	chr3:47891634-48019462	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv529989	chr3:47909480-48301481	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv1001056	chr3:47912342-48223849	Genic enhancers Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats 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	21 gene(s)	inside rSNPs	diseases
6	esv1796001	chr3:47912703-48012797	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv1826403	chr3:47912703-48012797	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv1835684	chr3:47912703-48123540	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
9	esv1827272	chr3:47912703-48260968	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	nsv1000817	chr3:47927730-48032401	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47910200-47957000	Weak transcription	Small Intestine	intestine
2	chr3:47910200-47978000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:47912600-47939200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr3:47915000-47939000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr3:47917600-47957400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:47919800-47937000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:47922000-47951400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:47926000-47935000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:47926800-47953400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr3:47926800-47957400	Weak transcription	Colonic Mucosa	Colon
11	chr3:47927000-47936800	Weak transcription	GM12878-XiMat	blood
12	chr3:47930000-47934000	Strong transcription	HMEC	breast
13	chr3:47930000-47934400	Strong transcription	HepG2	liver
14	chr3:47930000-47934600	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr3:47930000-47940000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:47930200-47937000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:47930200-47941600	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr3:47930400-47933800	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr3:47930400-47934200	Strong transcription	NHEK	skin
20	chr3:47930400-47935200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr3:47930600-47934000	Enhancers	Right Atrium	heart
22	chr3:47930600-47935000	Strong transcription	Primary B cells from cord blood	blood
23	chr3:47930600-47935000	Strong transcription	Primary T cells from cord blood	blood
24	chr3:47930800-47934000	Genic enhancers	Fetal Muscle Leg	muscle
25	chr3:47930800-47934400	Strong transcription	Hela-S3	cervix
26	chr3:47931000-47935800	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr3:47931200-47935000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:47931600-47933800	Strong transcription	Primary B cells from peripheral blood	blood
29	chr3:47931600-47933800	Flanking Active TSS	Brain Germinal Matrix	brain
30	chr3:47931600-47933800	Enhancers	Psoas Muscle	Psoas
31	chr3:47931600-47934600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr3:47931600-47935600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:47931800-47933600	Enhancers	Rectal Smooth Muscle	rectum
34	chr3:47931800-47934400	Flanking Active TSS	Brain Cingulate Gyrus	brain
35	chr3:47931800-47935800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
36	chr3:47932000-47933400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:47932000-47934000	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr3:47932000-47935000	Strong transcription	Fetal Intestine Small	intestine
39	chr3:47932000-47935200	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr3:47932000-47937200	Strong transcription	Osteobl	bone
41	chr3:47932000-47969200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr3:47932200-47933600	Genic enhancers	Placenta	Placenta
43	chr3:47932200-47933800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:47932200-47933800	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr3:47932200-47933800	Genic enhancers	Fetal Stomach	stomach
46	chr3:47932200-47933800	Strong transcription	Spleen	Spleen
47	chr3:47932200-47934000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr3:47932200-47934000	Strong transcription	NHLF	lung
49	chr3:47932200-47934200	Enhancers	H1 Cell Line	embryonic stem cell
50	chr3:47932200-47934200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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