Variant report

Variant	rs740787
Chromosome Location	chr3:48671578-48671579
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48671024-48673628	HepG2	liver:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48644319..48649140-chr3:48667292..48673836,7	K562	blood:
2	chr3:48592797..48594664-chr3:48671142..48674033,2	MCF-7	breast:
3	chr3:48620158..48621979-chr3:48670195..48672558,2	K562	blood:
4	chr3:48671184..48673366-chr3:48722826..48724747,2	K562	blood:
5	chr3:48608865..48611269-chr3:48670330..48672389,2	K562	blood:
6	chr3:48670869..48673258-chr3:48680752..48682540,2	K562	blood:
7	chr3:48670764..48674544-chr3:48698929..48702803,9	K562	blood:
8	chr3:48645687..48647354-chr3:48671015..48673103,2	MCF-7	breast:
9	chr3:48670764..48674544-chr3:48699167..48702803,6	K562	blood:
10	chr3:48671382..48674659-chr3:48676453..48680538,5	MCF-7	breast:
11	chr3:48665788..48669314-chr3:48669500..48672901,6	K562	blood:
12	chr17:73775608..73776222-chr3:48671105..48671727,2	HCT-116	colon:
13	chr3:48641673..48644998-chr3:48670911..48673807,4	K562	blood:
14	chr3:48669740..48673837-chr3:48676132..48680334,3	MCF-7	breast:
15	chr3:48670890..48672785-chr3:48672866..48675614,2	MCF-7	breast:
16	chr3:48670997..48674874-chr3:48698947..48702118,7	MCF-7	breast:
17	chr3:48541156..48543765-chr3:48670075..48672910,2	K562	blood:
18	chr3:48667529..48675453-chr3:48697968..48703139,10	MCF-7	breast:
19	chr3:48594247..48597141-chr3:48671392..48674077,2	MCF-7	breast:

No data

Variant related genes	Relation type
SLC26A6	TF binding region
ENSG00000164054	Chromatin interaction
ENSG00000114268	Chromatin interaction
ENSG00000132475	Chromatin interaction
ENSG00000228350	Chromatin interaction
ENSG00000008300	Chromatin interaction
ENSG00000010256	Chromatin interaction
ENSG00000263898	Chromatin interaction
ENSG00000213672	Chromatin interaction
ENSG00000114270	Chromatin interaction
ENSG00000225697	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1003649	0.83[GIH][hapmap]
rs10470687	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs11706983	1.00[GIH][hapmap];0.83[TSI][hapmap]
rs11708786	1.00[GIH][hapmap]
rs11713694	0.83[GIH][hapmap]
rs11719291	1.00[GIH][hapmap];0.83[TSI][hapmap]
rs12107252	0.94[ASW][hapmap];0.90[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12107418	0.94[ASW][hapmap];0.90[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12715429	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13060933	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13063312	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13070798	0.90[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13074318	0.83[GIH][hapmap]
rs13076269	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13091944	1.00[JPT][hapmap]
rs13096357	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13319651	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13324119	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13324142	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13434258	1.00[GIH][hapmap];0.83[TSI][hapmap]
rs17080289	0.90[CHD][hapmap];1.00[GIH][hapmap];0.84[ASN][1000 genomes]
rs2006871	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2276850	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2276852	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2286651	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2286652	0.90[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2302295	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2310996	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2310997	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28452701	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2854394	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs34037363	0.83[GIH][hapmap]
rs34096717	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34368826	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34638686	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35064573	1.00[GIH][hapmap];0.83[TSI][hapmap]
rs35343040	0.86[ASN][1000 genomes]
rs35796820	0.84[ASN][1000 genomes]
rs3733086	0.84[ASN][1000 genomes]
rs3806694	1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3821875	0.81[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3821876	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3969942	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs57334642	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6768448	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6773261	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6781283	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs6792156	0.82[ASW][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6792525	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs68042649	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6806059	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs7428949	1.00[JPT][hapmap]
rs7620853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631574	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809222	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9810549	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9810991	0.89[CHD][hapmap];0.83[GIH][hapmap]
rs9811318	0.83[ASW][hapmap];0.90[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9812200	1.00[ASW][hapmap];0.90[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9821797	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9830581	0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9836462	0.89[ASW][hapmap];0.90[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9837687	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9841602	0.89[ASW][hapmap];0.90[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9843316	0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9850102	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9851771	0.83[GIH][hapmap]
rs9868809	0.90[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9869698	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9871180	0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs9873726	0.86[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9875911	0.83[GIH][hapmap]
rs9878063	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9878950	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9881877	0.85[CHD][hapmap];1.00[GIH][hapmap]
rs9882549	1.00[GIH][hapmap]
rs9882962	0.80[CHD][hapmap];0.83[GIH][hapmap]

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	esv3430072	chr3:48668048-48673146	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	14 gene(s)	inside rSNPs	diseases
9	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs740787	SLC26A6	cis	lung	GTEx
rs740787	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs740787	WDR6	cis	lung	GTEx
rs740787	WDR6	cis	Esophagus Mucosa	GTEx
rs740787	WDR6	cis	lymphoblastoid	seeQTL
rs740787	WDR6	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48649000-48672000	Weak transcription	Fetal Brain Male	brain
2	chr3:48661000-48671600	Weak transcription	Psoas Muscle	Psoas
3	chr3:48661200-48671800	Weak transcription	Small Intestine	intestine
4	chr3:48661800-48671600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:48662000-48671800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr3:48662200-48671800	Weak transcription	Primary B cells from cord blood	blood
7	chr3:48662200-48671800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr3:48665800-48671600	Weak transcription	K562	blood
9	chr3:48665800-48671800	Weak transcription	HSMMtube	muscle
10	chr3:48666600-48671800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr3:48667400-48671800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:48668200-48671800	Weak transcription	A549	lung
13	chr3:48669400-48671800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:48669400-48671800	Weak transcription	HUVEC	blood vessel
15	chr3:48669800-48671600	Weak transcription	Brain Substantia Nigra	brain
16	chr3:48669800-48671800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:48670000-48673200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:48670200-48671600	Weak transcription	Primary T cells from cord blood	blood
19	chr3:48670200-48671600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:48670200-48671800	Genic enhancers	Spleen	Spleen
21	chr3:48670400-48671600	Weak transcription	Fetal Lung	lung
22	chr3:48670600-48671600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:48670600-48671600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:48670600-48671600	Weak transcription	Osteobl	bone
25	chr3:48670600-48671800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:48670800-48671600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:48670800-48671600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:48670800-48671600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr3:48670800-48671600	Weak transcription	HSMM	muscle
30	chr3:48670800-48671600	Genic enhancers	Monocytes-CD14+_RO01746	blood
31	chr3:48670800-48671800	Weak transcription	Brain Anterior Caudate	brain
32	chr3:48670800-48672000	Weak transcription	Thymus	Thymus
33	chr3:48671000-48671600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr3:48671000-48671600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:48671000-48671600	Weak transcription	Brain Hippocampus Middle	brain
36	chr3:48671000-48671600	Enhancers	HMEC	breast
37	chr3:48671000-48671800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:48671000-48671800	Weak transcription	Right Ventricle	heart
39	chr3:48671000-48672000	Enhancers	Primary T cells fromperipheralblood	blood
40	chr3:48671000-48672000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr3:48671000-48672000	Weak transcription	Fetal Brain Female	brain
42	chr3:48671000-48672200	Enhancers	Pancreas	Pancrea
43	chr3:48671200-48671600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr3:48671200-48671600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr3:48671200-48671600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:48671200-48671600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
47	chr3:48671200-48671600	Enhancers	GM12878-XiMat	blood
48	chr3:48671200-48671800	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr3:48671200-48671800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr3:48671200-48671800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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