Variant report

Variant	rs7199680
Chromosome Location	chr16:75355957-75355958
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1017239	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1074961	0.91[ASN][1000 genomes]
rs10781977	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10871307	0.87[ASN][1000 genomes]
rs10871308	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11149812	0.85[ASN][1000 genomes]
rs11149813	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11149814	0.86[ASN][1000 genomes]
rs11149816	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11645691	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11646418	0.94[ASN][1000 genomes]
rs12445188	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12445211	0.91[ASN][1000 genomes]
rs12445813	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12446903	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12449177	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12922897	0.87[EUR][1000 genomes]
rs12932952	0.90[ASN][1000 genomes]
rs12935329	0.90[ASN][1000 genomes]
rs1862705	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1895489	0.84[ASN][1000 genomes]
rs2032926	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2059257	0.88[ASN][1000 genomes]
rs247423	0.85[ASN][1000 genomes]
rs247424	0.84[ASN][1000 genomes]
rs247425	0.84[ASN][1000 genomes]
rs247427	0.89[ASN][1000 genomes]
rs247431	0.89[ASN][1000 genomes]
rs247434	0.88[ASN][1000 genomes]
rs247436	0.89[ASN][1000 genomes]
rs247437	0.87[ASN][1000 genomes]
rs247438	0.89[ASN][1000 genomes]
rs2865527	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2865532	0.90[ASN][1000 genomes]
rs3743606	0.84[ASN][1000 genomes]
rs3784936	0.88[ASN][1000 genomes]
rs3784937	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3844219	0.90[ASN][1000 genomes]
rs3851735	0.94[ASN][1000 genomes]
rs3851736	0.90[ASN][1000 genomes]
rs3851739	0.86[ASN][1000 genomes]
rs4536500	0.88[ASN][1000 genomes]
rs455407	0.89[ASN][1000 genomes]
rs467223	0.88[ASN][1000 genomes]
rs467780	0.88[ASN][1000 genomes]
rs468079	0.89[ASN][1000 genomes]
rs4887813	0.84[ASN][1000 genomes]
rs4887814	0.86[ASN][1000 genomes]
rs4888374	0.85[ASN][1000 genomes]
rs4888375	0.85[ASN][1000 genomes]
rs4888381	0.94[ASN][1000 genomes]
rs4888393	0.88[ASN][1000 genomes]
rs4888394	0.88[ASN][1000 genomes]
rs4888395	0.88[ASN][1000 genomes]
rs4888396	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4888397	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4888398	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4993971	0.88[ASN][1000 genomes]
rs6564249	0.93[ASN][1000 genomes]
rs6564256	0.86[ASN][1000 genomes]
rs7189407	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7192155	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7202284	0.92[ASN][1000 genomes]
rs766522	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8046184	0.88[ASN][1000 genomes]
rs8046949	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8048677	0.89[ASN][1000 genomes]
rs8048816	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8049611	0.88[ASN][1000 genomes]
rs8050662	0.92[ASN][1000 genomes]
rs8051611	0.90[ASN][1000 genomes]
rs8051785	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8053632	0.90[ASN][1000 genomes]
rs8054586	0.88[ASN][1000 genomes]
rs8055609	0.89[ASN][1000 genomes]
rs889446	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9933956	0.94[ASN][1000 genomes]
rs9934007	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9989421	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
3	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
4	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
5	nsv833283	chr16:75302175-75392308	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7199680	CFDP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75317400-75358000	Weak transcription	Fetal Brain Male	brain
2	chr16:75338800-75426400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr16:75339200-75358000	Weak transcription	Brain Germinal Matrix	brain
4	chr16:75339400-75411800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr16:75340400-75374800	Weak transcription	Aorta	Aorta
6	chr16:75340800-75357800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr16:75340800-75373400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr16:75341800-75364600	Weak transcription	Hela-S3	cervix
9	chr16:75342200-75357200	Weak transcription	Placenta	Placenta
10	chr16:75342200-75381200	Weak transcription	Esophagus	oesophagus
11	chr16:75344000-75376400	Weak transcription	Gastric	stomach
12	chr16:75344600-75361400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr16:75344800-75359000	Weak transcription	Psoas Muscle	Psoas
14	chr16:75345600-75357200	Weak transcription	A549	lung
15	chr16:75347600-75358200	Weak transcription	Fetal Brain Female	brain
16	chr16:75347600-75366000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr16:75347800-75357800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr16:75348400-75374200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr16:75351600-75363200	Weak transcription	HepG2	liver
20	chr16:75352000-75361200	Weak transcription	Fetal Stomach	stomach
21	chr16:75352000-75368000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr16:75352200-75357800	Weak transcription	Fetal Kidney	kidney
23	chr16:75352200-75362600	Weak transcription	Fetal Intestine Large	intestine
24	chr16:75352200-75376400	Weak transcription	Pancreas	Pancrea
25	chr16:75352200-75396000	Weak transcription	Lung	lung
26	chr16:75352400-75358000	Weak transcription	K562	blood
27	chr16:75353400-75358000	Enhancers	NHEK	skin
28	chr16:75353800-75357400	Weak transcription	Fetal Intestine Small	intestine
29	chr16:75354200-75356200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr16:75354600-75356000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr16:75354600-75356200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr16:75354600-75356200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr16:75354600-75356600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr16:75354600-75356600	Enhancers	HSMM	muscle
35	chr16:75354600-75357200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr16:75354600-75357400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr16:75354600-75357600	Enhancers	Muscle Satellite Cultured Cells	--
38	chr16:75354600-75357600	Weak transcription	Adipose Nuclei	Adipose
39	chr16:75354600-75358200	Enhancers	NHLF	lung
40	chr16:75354600-75358400	Enhancers	HMEC	breast
41	chr16:75354600-75362800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr16:75354600-75367800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr16:75354600-75373400	Weak transcription	Left Ventricle	heart
44	chr16:75354600-75375000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr16:75354800-75356200	Weak transcription	Fetal Heart	heart
46	chr16:75354800-75357200	Weak transcription	Ovary	ovary
47	chr16:75354800-75357400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr16:75354800-75357400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr16:75354800-75357400	Enhancers	NHDF-Ad	bronchial
50	chr16:75354800-75357600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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