Variant report

Variant	rs4247109
Chromosome Location	chr16:69803443-69803444
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:69801430..69804144-chr16:69805898..69809751,3	K562	blood:
2	chr16:69797842..69799591-chr16:69801764..69803595,2	K562	blood:
3	chr16:69797849..69800975-chr16:69802964..69805874,3	MCF-7	breast:
4	chr16:69801326..69804144-chr16:69805460..69809751,5	K562	blood:

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10400956	0.93[ASN][1000 genomes]
rs10517	0.82[ASW][hapmap];0.81[CHD][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs11075736	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1139177	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11862697	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs12019048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs12149920	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12921017	0.88[EUR][1000 genomes]
rs1318651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13329844	0.81[CHD][hapmap]
rs16958997	0.84[CHD][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap]
rs16959059	0.82[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs16959266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16959271	0.81[ASN][1000 genomes]
rs2088747	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[ASN][1000 genomes]
rs2291960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.88[ASN][1000 genomes]
rs2304526	0.84[CHD][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap]
rs2917665	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2917667	0.82[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2917669	1.00[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs2917673	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2917674	0.90[EUR][1000 genomes]
rs2917675	0.83[EUR][1000 genomes]
rs2917676	0.88[EUR][1000 genomes]
rs2917681	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2917682	0.88[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.87[LWK][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs2917683	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs2937120	0.88[ASN][1000 genomes]
rs2937123	0.88[ASN][1000 genomes]
rs2937126	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.91[ASN][1000 genomes]
rs2937127	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2965752	0.83[AMR][1000 genomes]
rs2965753	0.82[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap]
rs2965756	0.88[ASN][1000 genomes]
rs2965759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2965760	0.86[ASN][1000 genomes]
rs2965761	0.86[ASN][1000 genomes]
rs2965762	0.89[ASN][1000 genomes]
rs2965763	0.89[ASN][1000 genomes]
rs2965764	0.89[ASN][1000 genomes]
rs3790084	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3790087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3790088	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.87[ASN][1000 genomes]
rs3826154	0.87[CEU][hapmap];0.84[CHD][hapmap];1.00[MEX][hapmap]
rs4247107	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4442796	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4608327	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4619391	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4985527	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.85[ASN][1000 genomes]
rs4985528	0.80[ASN][1000 genomes]
rs4985529	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4985531	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61090597	0.86[ASN][1000 genomes]
rs6499246	0.83[EUR][1000 genomes]
rs6499248	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6499249	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6499250	0.95[ASN][1000 genomes]
rs6499259	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.89[ASN][1000 genomes]
rs689452	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs689456	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7188187	0.89[ASN][1000 genomes]
rs7204615	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7359387	0.88[CEU][hapmap];0.84[CHD][hapmap];1.00[MEX][hapmap]
rs8050369	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8052459	0.82[ASN][1000 genomes]
rs8057938	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8058594	0.88[ASN][1000 genomes]
rs8062076	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9888980	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs9888981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9888993	0.84[CHD][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap]
rs9889219	0.84[CHD][hapmap]
rs9922223	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs9924953	0.84[CHD][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap]
rs9927105	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9932486	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9934681	0.84[CHD][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap]
rs9936464	0.84[CHD][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap]
rs9940008	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv524364	chr16:69745145-69803443	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4247109	GFOD2	cis	parietal	SCAN
rs4247109	FUK	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69797200-69803800	Weak transcription	Lung	lung
2	chr16:69797200-69806200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr16:69797200-69807000	Weak transcription	Esophagus	oesophagus
4	chr16:69797200-69807000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr16:69797200-69809800	Weak transcription	Small Intestine	intestine
6	chr16:69797400-69806400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr16:69797400-69806400	Weak transcription	Brain Substantia Nigra	brain
8	chr16:69797400-69806600	Weak transcription	Brain Angular Gyrus	brain
9	chr16:69797400-69821200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr16:69797600-69806400	Weak transcription	HSMM	muscle
11	chr16:69797600-69806600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr16:69797600-69808200	Weak transcription	Primary T cells from cord blood	blood
13	chr16:69797600-69816800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr16:69797600-69853400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr16:69797800-69803600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr16:69797800-69804400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr16:69797800-69806200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr16:69797800-69806200	Weak transcription	Hela-S3	cervix
19	chr16:69797800-69806400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr16:69797800-69806600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr16:69797800-69806600	Weak transcription	Adipose Nuclei	Adipose
22	chr16:69797800-69806600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr16:69797800-69806600	Weak transcription	K562	blood
24	chr16:69797800-69806800	Weak transcription	NH-A	brain
25	chr16:69797800-69809200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr16:69797800-69809200	Weak transcription	A549	lung
27	chr16:69797800-69809800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr16:69797800-69821200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr16:69798000-69804400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr16:69798000-69804800	Weak transcription	Primary B cells from cord blood	blood
31	chr16:69798000-69806400	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr16:69798000-69806400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr16:69798000-69806400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr16:69798000-69806400	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr16:69798000-69806600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr16:69798000-69806600	Weak transcription	HSMMtube	muscle
37	chr16:69798000-69809200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr16:69798000-69809400	Weak transcription	Dnd41	blood
39	chr16:69798000-69810000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr16:69798200-69805400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr16:69798200-69805600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr16:69798400-69803600	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr16:69798400-69804000	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr16:69798400-69806400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr16:69798600-69806400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr16:69799800-69803800	Enhancers	HepG2	liver
47	chr16:69800400-69805200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr16:69800600-69804000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr16:69800600-69805600	Weak transcription	Pancreas	Pancrea
50	chr16:69800600-69806000	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links