Variant report

Variant	rs6769978
Chromosome Location	chr3:24434851-24434852
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:24428751..24431920-chr3:24433157..24435631,4	K562	blood:
2	chr3:24421950..24424511-chr3:24434114..24437100,2	K562	blood:
3	chr3:24416630..24419472-chr3:24433631..24435823,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11129152	0.99[ASN][1000 genomes]
rs11918018	0.97[ASN][1000 genomes]
rs12495379	0.82[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs13065876	0.95[ASN][1000 genomes]
rs13086388	0.97[ASN][1000 genomes]
rs1505286	0.84[ASN][1000 genomes]
rs1505287	0.84[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs1505289	0.84[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs17014597	0.84[ASN][1000 genomes]
rs17014605	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs28380451	0.95[ASN][1000 genomes]
rs35340172	0.94[ASN][1000 genomes]
rs4300958	0.99[ASN][1000 genomes]
rs4309672	0.97[ASN][1000 genomes]
rs4331621	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4423711	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4491844	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4541352	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs4602332	0.94[ASN][1000 genomes]
rs4630886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858608	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs4858610	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60904521	0.81[EUR][1000 genomes]
rs6550865	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6771995	0.99[ASN][1000 genomes]
rs6786474	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7611219	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7630858	0.99[ASN][1000 genomes]
rs7648757	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9310740	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs9816509	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834640	chr3:24339779-24493605	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24420200-24441600	Weak transcription	Liver	Liver
2	chr3:24430400-24437200	Weak transcription	K562	blood
3	chr3:24430600-24443600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:24431600-24435800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:24431600-24437800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:24431600-24437800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:24431600-24438200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:24431800-24442800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:24432200-24440800	Weak transcription	Stomach Mucosa	stomach
10	chr3:24432200-24445200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:24432600-24442000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:24432600-24448400	Weak transcription	Gastric	stomach
13	chr3:24432600-24448600	Weak transcription	Right Ventricle	heart
14	chr3:24432800-24435000	Weak transcription	Left Ventricle	heart
15	chr3:24432800-24440800	Weak transcription	Fetal Intestine Large	intestine
16	chr3:24432800-24440800	Weak transcription	Fetal Intestine Small	intestine
17	chr3:24432800-24443200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:24433600-24435800	Weak transcription	Aorta	Aorta
19	chr3:24434000-24435400	Enhancers	Fetal Kidney	kidney
20	chr3:24434600-24435200	Enhancers	H9 Cell Line	embryonic stem cell
21	chr3:24434600-24435200	Enhancers	Fetal Lung	lung
22	chr3:24434600-24435200	Enhancers	Rectal Smooth Muscle	rectum
23	chr3:24434600-24435400	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr3:24434600-24435400	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr3:24434600-24435400	Enhancers	Colon Smooth Muscle	Colon
26	chr3:24434800-24435000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:24434800-24435200	Enhancers	Psoas Muscle	Psoas
28	chr3:24434800-24435200	Flanking Active TSS	HepG2	liver
29	chr3:24434800-24435400	Enhancers	Pancreas	Pancrea
30	chr3:24434800-24435400	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr3:24434800-24435400	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links