Variant report

Variant	rs3789592
Chromosome Location	chr1:113471400-113471401
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10158127	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1049434	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10776763	0.95[ASN][1000 genomes]
rs10857980	0.96[CEU][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs10857982	0.94[ASN][1000 genomes]
rs10857983	0.94[ASN][1000 genomes]
rs11102562	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11102565	0.94[ASN][1000 genomes]
rs11102568	0.88[ASN][1000 genomes]
rs12028967	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12037621	0.90[ASN][1000 genomes]
rs1216603	0.86[EUR][1000 genomes]
rs1539624	0.96[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1627925	0.82[EUR][1000 genomes]
rs1629027	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1728218	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs1728219	0.82[EUR][1000 genomes]
rs1728232	0.82[EUR][1000 genomes]
rs1983929	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs2096301	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2105388	0.91[EUR][1000 genomes]
rs2769259	0.80[EUR][1000 genomes]
rs2996295	0.87[ASW][hapmap];0.92[MEX][hapmap]
rs4301628	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4838969	0.85[EUR][1000 genomes]
rs4838970	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4839273	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6537762	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6537764	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6537765	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6663872	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6670224	0.90[CEU][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6681037	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6681552	0.91[EUR][1000 genomes]
rs7169	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7551223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7556664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs773430	0.84[EUR][1000 genomes]
rs773432	0.84[EUR][1000 genomes]
rs773433	0.84[EUR][1000 genomes]
rs773434	0.83[EUR][1000 genomes]
rs773435	0.84[EUR][1000 genomes]
rs773436	0.83[EUR][1000 genomes]
rs773439	0.82[EUR][1000 genomes]
rs773442	0.86[EUR][1000 genomes]
rs9633370	0.96[CEU][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[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	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	nsv997426	chr1:113288282-113639507	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer 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	68 gene(s)	inside rSNPs	diseases
9	nsv1004102	chr1:113295805-113551210	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
10	esv3399982	chr1:113358580-113542255	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
11	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
12	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
13	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3789592	AMPD1	cis	parietal	SCAN
rs3789592	OLFML3	cis	cerebellum	SCAN
rs3789592	SLC6A17	cis	parietal	SCAN
rs3789592	DENND2C	cis	parietal	SCAN
rs3789592	DENND2C	cis	cerebellum	SCAN
rs3789592	LRIG2	cis	cerebellum	SCAN
rs3789592	OVGP1	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113449600-113474600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:113449600-113477200	Weak transcription	Stomach Mucosa	stomach
3	chr1:113451400-113475400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:113452800-113473000	Strong transcription	Dnd41	blood
5	chr1:113452800-113476600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:113455800-113472200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:113456200-113473000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:113456400-113472400	Weak transcription	Primary B cells from peripheral blood	blood
9	chr1:113456600-113472800	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr1:113458000-113490600	Weak transcription	Right Atrium	heart
11	chr1:113458200-113473000	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:113458200-113473400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:113458400-113473000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:113458400-113473000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:113458600-113478400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:113458800-113472400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:113458800-113472400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:113460200-113475400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:113460400-113472400	Weak transcription	Small Intestine	intestine
20	chr1:113460400-113479800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:113460400-113481000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:113460600-113473200	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr1:113460600-113477200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:113460600-113478400	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:113460800-113480200	Weak transcription	Adipose Nuclei	Adipose
26	chr1:113460800-113480600	Weak transcription	Ovary	ovary
27	chr1:113461000-113477200	Weak transcription	Fetal Intestine Large	intestine
28	chr1:113461200-113478400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:113462400-113472000	Strong transcription	NHEK	skin
30	chr1:113464000-113472000	Strong transcription	HSMM	muscle
31	chr1:113464200-113473000	Strong transcription	K562	blood
32	chr1:113464800-113473000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:113464800-113477800	Weak transcription	NH-A	brain
34	chr1:113465200-113473000	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr1:113466000-113472000	Strong transcription	Fetal Thymus	thymus
36	chr1:113466000-113472400	Strong transcription	Hela-S3	cervix
37	chr1:113466200-113473400	Weak transcription	Placenta	Placenta
38	chr1:113466400-113496400	Weak transcription	Primary T cells from cord blood	blood
39	chr1:113466800-113471600	Weak transcription	Right Ventricle	heart
40	chr1:113466800-113479800	Weak transcription	Fetal Lung	lung
41	chr1:113467000-113471600	Weak transcription	Fetal Muscle Leg	muscle
42	chr1:113467000-113472600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr1:113467000-113473000	Weak transcription	Brain Germinal Matrix	brain
44	chr1:113467000-113473400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr1:113467000-113473600	Weak transcription	Colonic Mucosa	Colon
46	chr1:113467000-113477200	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr1:113467000-113478000	Weak transcription	NHLF	lung
48	chr1:113467000-113478400	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr1:113467000-113479600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:113467000-113480200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links