Variant report

Variant	rs2310996
Chromosome Location	chr3:48671834-48671835
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr3:48671808-48673623	Hela-S3	cervix:	n/a	n/a
2	MXI1	chr3:48671725-48673948	IMR90	lung:	n/a	n/a
3	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	chr3:48641673..48644998-chr3:48670911..48673807,4	K562	blood:
13	chr3:48669740..48673837-chr3:48676132..48680334,3	MCF-7	breast:
14	chr3:48631939..48633856-chr3:48671693..48673580,2	K562	blood:
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
ENSG00000114268	Chromatin interaction
ENSG00000114270	Chromatin interaction
ENSG00000225697	Chromatin interaction
ENSG00000010256	Chromatin interaction
ENSG00000213672	Chromatin interaction
ENSG00000263898	Chromatin interaction
ENSG00000008300	Chromatin interaction
ENSG00000228350	Chromatin interaction
ENSG00000164054	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	1.00[ASW][hapmap];0.90[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12107418	1.00[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];0.80[AFR][1000 genomes];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	0.94[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];1.00[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[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]
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	0.90[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]
rs740787	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]
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	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.90[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	0.88[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	0.94[ASW][hapmap];0.90[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[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	0.82[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	0.82[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	0.91[AFR][1000 genomes];0.98[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
rs2310996	WDR6	cis	Adipose Subcutaneous	GTEx
rs2310996	SLC26A6	cis	lung	GTEx
rs2310996	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs2310996	WDR6	cis	Esophagus Mucosa	GTEx
rs2310996	WDR6	cis	lymphoblastoid	seeQTL
rs2310996	WDR6	cis	lung	GTEx

Chromatin state (count:126 , 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	chr3:48670000-48673200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:48670800-48672000	Weak transcription	Thymus	Thymus
4	chr3:48671000-48672000	Enhancers	Primary T cells fromperipheralblood	blood
5	chr3:48671000-48672000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr3:48671000-48672000	Weak transcription	Fetal Brain Female	brain
7	chr3:48671000-48672200	Enhancers	Pancreas	Pancrea
8	chr3:48671200-48672000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:48671200-48672000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr3:48671200-48672000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:48671200-48672000	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr3:48671200-48672000	Enhancers	Fetal Muscle Trunk	muscle
13	chr3:48671200-48672000	Enhancers	Placenta	Placenta
14	chr3:48671200-48672000	Enhancers	Ovary	ovary
15	chr3:48671200-48672000	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr3:48671200-48672200	Weak transcription	Lung	lung
17	chr3:48671200-48672400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:48671200-48672400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:48671200-48672400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:48671200-48672400	Flanking Active TSS	Dnd41	blood
21	chr3:48671200-48672400	Flanking Active TSS	Hela-S3	cervix
22	chr3:48671400-48672000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:48671400-48672000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:48671400-48672000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:48671400-48672000	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr3:48671400-48672000	Enhancers	Primary hematopoietic stem cells	blood
27	chr3:48671400-48672000	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr3:48671400-48672000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:48671400-48672000	Enhancers	Adipose Nuclei	Adipose
30	chr3:48671400-48672000	Enhancers	Liver	Liver
31	chr3:48671400-48672000	Enhancers	Brain Angular Gyrus	brain
32	chr3:48671400-48672000	Enhancers	Brain Germinal Matrix	brain
33	chr3:48671400-48672000	Enhancers	Fetal Thymus	thymus
34	chr3:48671400-48672000	Enhancers	Left Ventricle	heart
35	chr3:48671400-48672000	Enhancers	Placenta Amnion	Placenta Amnion
36	chr3:48671400-48672200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:48671400-48672200	Flanking Active TSS	Fetal Intestine Large	intestine
38	chr3:48671400-48672200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
39	chr3:48671400-48672400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:48671400-48672400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:48671400-48672400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr3:48671400-48673600	Active TSS	Gastric	stomach
43	chr3:48671400-48674400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr3:48671600-48672000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr3:48671600-48672000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:48671600-48672000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:48671600-48672000	Enhancers	Brain Cingulate Gyrus	brain
48	chr3:48671600-48672000	Enhancers	Brain Substantia Nigra	brain
49	chr3:48671600-48672000	Enhancers	Fetal Lung	lung
50	chr3:48671600-48672000	Enhancers	Fetal Muscle Leg	muscle

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