Variant report

Variant	rs3821875
Chromosome Location	chr3:48697654-48697655
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48697535-48697802	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:48697491-48698052	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:48697601-48697893	MCF-7	breast:	n/a	n/a
4	POLR2A	chr3:48697356-48697878	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr3:48697354-48698199	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48686766..48690063-chr3:48696074..48699163,3	MCF-7	breast:
2	chr3:48695950..48699824-chr3:48710158..48713070,3	K562	blood:
3	chr3:48678686..48681268-chr3:48696483..48698297,2	K562	blood:
4	chr3:48659070..48661619-chr3:48697247..48699239,2	K562	blood:
5	chr3:48678686..48683466-chr3:48696483..48700259,5	K562	blood:
6	chr3:48686566..48688475-chr3:48697453..48700260,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000228350	TF binding region
ENSG00000263898	Chromatin interaction
ENSG00000008300	Chromatin interaction
ENSG00000183396	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10470687	1.00[JPT][hapmap]
rs11557629	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11706203	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11706983	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11708786	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11715177	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11719291	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12107252	0.81[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12107418	0.81[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12715429	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13060933	1.00[JPT][hapmap]
rs13063223	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13063312	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13070798	0.81[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13076269	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13086240	0.82[AMR][1000 genomes]
rs13090013	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13091944	1.00[JPT][hapmap]
rs13096357	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13316551	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13319651	1.00[JPT][hapmap]
rs13324119	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13324142	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13324950	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13434258	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17080319	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2006871	1.00[JPT][hapmap]
rs2276850	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2276852	0.81[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2286651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286652	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302295	0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2310996	0.81[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2310997	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28452701	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2854394	1.00[JPT][hapmap]
rs28567949	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28657585	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28793701	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34096717	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34153629	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34368826	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34577723	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34638686	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35064573	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3733086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3806694	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3821876	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4077495	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56735597	0.80[AMR][1000 genomes]
rs57334642	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6768448	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6773261	1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6781283	1.00[JPT][hapmap]
rs6792156	1.00[JPT][hapmap]
rs6792525	1.00[JPT][hapmap]
rs68042649	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6806059	1.00[JPT][hapmap]
rs73078349	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73078362	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs740787	0.81[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7428949	1.00[JPT][hapmap]
rs7620853	1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7631574	0.81[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9809222	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9810549	1.00[JPT][hapmap]
rs9811027	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9811318	0.81[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9812200	0.81[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9812977	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9821797	1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9830581	1.00[JPT][hapmap]
rs9834996	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9836462	0.81[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9837687	1.00[JPT][hapmap]
rs9841602	0.81[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9843316	1.00[JPT][hapmap]
rs9850102	1.00[JPT][hapmap]
rs9854034	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9868809	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9869698	1.00[JPT][hapmap]
rs9871180	1.00[JPT][hapmap]
rs9873726	1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9877542	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9877685	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9878063	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9878950	1.00[JPT][hapmap]
rs9881877	1.00[JPT][hapmap]
rs9882549	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS 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	53 gene(s)	inside rSNPs	diseases
5	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv590246	chr3:48628014-48721040	Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv876763	chr3:48669648-48710310	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	esv3359935	chr3:48696498-48699296	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3821875	WDR6	cis	Esophagus Mucosa	GTEx
rs3821875	SLC26A6	cis	lung	GTEx
rs3821875	WDR6	cis	Adipose Subcutaneous	GTEx
rs3821875	WDR6	cis	Whole Blood	GTEx
rs3821875	WDR6	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48694000-48698800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:48694200-48698400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:48694200-48698600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:48694200-48698600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:48694200-48698600	Weak transcription	HSMMtube	muscle
6	chr3:48694200-48699000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:48694400-48698200	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:48694400-48698600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:48694400-48698600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:48694400-48698800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:48694400-48698800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:48694400-48698800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr3:48694400-48698800	Weak transcription	HUVEC	blood vessel
14	chr3:48694600-48698800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr3:48694600-48698800	Weak transcription	Brain Substantia Nigra	brain
16	chr3:48694800-48698600	Weak transcription	Left Ventricle	heart
17	chr3:48694800-48698800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr3:48694800-48698800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:48694800-48698800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:48695000-48698200	Weak transcription	Pancreas	Pancrea
21	chr3:48695000-48698200	Weak transcription	Right Ventricle	heart
22	chr3:48695000-48698800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:48695400-48698600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:48695600-48698000	Genic enhancers	Brain Germinal Matrix	brain
25	chr3:48695600-48698200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:48695600-48698400	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:48695600-48698400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:48695800-48698000	Strong transcription	Brain Anterior Caudate	brain
29	chr3:48695800-48698200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:48695800-48698400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr3:48695800-48698400	Strong transcription	Brain Cingulate Gyrus	brain
32	chr3:48696200-48697800	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr3:48696200-48698400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:48696200-48698400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:48696200-48698600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:48696200-48698800	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr3:48696400-48698000	Strong transcription	HepG2	liver
38	chr3:48696400-48698400	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr3:48696400-48698600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:48696600-48698600	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr3:48696800-48697800	Strong transcription	A549	lung
42	chr3:48696800-48698000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:48696800-48698600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:48696800-48698600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:48696800-48699000	Enhancers	Spleen	Spleen
46	chr3:48697200-48697800	Genic enhancers	Fetal Brain Male	brain
47	chr3:48697200-48699000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:48697400-48697800	Strong transcription	Brain Hippocampus Middle	brain
49	chr3:48697400-48698000	Genic enhancers	Fetal Brain Female	brain
50	chr3:48697600-48698200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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