Variant report

Variant	rs9934440
Chromosome Location	chr16:70439105-70439106
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:70435074..70439461-chr16:70440189..70443531,4	K562	blood:
2	chr16:70437013..70440067-chr16:70462393..70466171,3	K562	blood:
3	chr16:70438164..70441046-chr16:70466223..70468146,2	K562	blood:
4	chr16:70413307..70415302-chr16:70438636..70441373,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260111	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 58 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11075767	0.85[CHD][hapmap];0.95[JPT][hapmap]
rs11075770	0.84[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs11641683	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11643373	0.94[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs11645437	0.95[JPT][hapmap]
rs11645585	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11648402	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs11866400	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs12102803	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12446395	0.85[CEU][hapmap]
rs12447090	0.88[CHD][hapmap];0.91[JPT][hapmap]
rs12597401	0.89[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs12925729	0.84[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs2070203	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs2168606	0.83[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2288491	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2303792	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs2303793	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs34087264	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs3762171	0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs3852695	0.92[ASN][1000 genomes]
rs3859068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4284632	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4436771	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4513092	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4985407	0.93[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap]
rs6499320	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs7189474	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs7192268	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs7200430	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs7201750	0.84[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs7204583	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs722579	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs7919	0.83[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs8049641	0.89[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs8051506	0.89[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs8052125	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs8053436	0.89[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs8057610	0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs8058224	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8062178	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs8062183	0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs8063690	0.85[ASN][1000 genomes]
rs8063990	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs8064013	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs936994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9927553	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9936225	0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs9939726	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv482577	chr16:70329048-70516069	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
2	nsv833272	chr16:70369769-70569723	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:58)

SNP	Gene	Cis/trans	Tissue	Source
rs9934440	RP11-296I10.6	cis	Artery Tibial	GTEx
rs9934440	PDXDC2P	cis	Artery Tibial	GTEx
rs9934440	RP11-419C5.2	cis	Esophagus Muscularis	GTEx
rs9934440	RP11-296I10.6	cis	lung	GTEx
rs9934440	RP11-419C5.2	cis	Muscle Skeletal	GTEx
rs9934440	CLEC18A	cis	Whole Blood	GTEx
rs9934440	PDXDC2P	cis	parietal	SCAN
rs9934440	CLEC18A	cis	Artery Tibial	GTEx
rs9934440	RP11-296I10.6	cis	Nerve Tibial	GTEx
rs9934440	PDXDC2P	cis	Nerve Tibial	GTEx
rs9934440	CLEC18A	cis	Adipose Subcutaneous	GTEx
rs9934440	CLEC18C	cis	Artery Tibial	GTEx
rs9934440	PDXDC2P	cis	Thyroid	GTEx
rs9934440	PDXDC2P	cis	Skin Sun Exposed Lower leg	GTEx
rs9934440	NFAT5	cis	cerebellum	SCAN
rs9934440	EXOSC6	cis	Artery Aorta	GTEx
rs9934440	PDXDC2P	cis	Artery Aorta	GTEx
rs9934440	TMCO7	cis	parietal	SCAN
rs9934440	CLEC18A	cis	lung	GTEx
rs9934440	RP11-296I10.6	cis	Stomach	GTEx
rs9934440	PDXDC2P	cis	Esophagus Muscularis	GTEx
rs9934440	EXOSC6	cis	Skin Sun Exposed Lower leg	GTEx
rs9934440	RP11-296I10.6	cis	Whole Blood	GTEx
rs9934440	RP11-296I10.6	cis	Skin Sun Exposed Lower leg	GTEx
rs9934440	EXOSC6	cis	Thyroid	GTEx
rs9934440	RP11-296I10.6	cis	Muscle Skeletal	GTEx
rs9934440	EXOSC6	cis	cerebellum	SCAN
rs9934440	EXOSC6	cis	Nerve Tibial	GTEx
rs9934440	AARS	Cis_1M	lymphoblastoid	RTeQTL
rs9934440	EXOSC6	cis	Adipose Subcutaneous	GTEx
rs9934440	RP11-419C5.2	cis	Skin Sun Exposed Lower leg	GTEx
rs9934440	EXOSC6	cis	Whole Blood	GTEx
rs9934440	PDXDC2P	cis	lung	GTEx
rs9934440	RP11-296I10.6	cis	Esophagus Muscularis	GTEx
rs9934440	CLEC18C	cis	Whole Blood	GTEx
rs9934440	RP11-419C5.2	cis	Adipose Subcutaneous	GTEx
rs9934440	RP11-419C5.2	cis	lung	GTEx
rs9934440	CLEC18A	cis	Thyroid	GTEx
rs9934440	CLEC18A	cis	Esophagus Mucosa	GTEx
rs9934440	CLEC18A	cis	Skin Sun Exposed Lower leg	GTEx
rs9934440	EXOSC6	cis	Stomach	GTEx
rs9934440	PDXDC2P	cis	Muscle Skeletal	GTEx
rs9934440	CLEC18C	cis	Nerve Tibial	GTEx
rs9934440	PDXDC2P	cis	Adipose Subcutaneous	GTEx
rs9934440	EXOSC6	cis	Artery Tibial	GTEx
rs9934440	RP11-419C5.2	cis	Nerve Tibial	GTEx
rs9934440	WWP2	cis	parietal	SCAN
rs9934440	EXOSC6	cis	Esophagus Muscularis	GTEx
rs9934440	EXOSC6	cis	parietal	SCAN
rs9934440	EXOSC6	cis	Esophagus Mucosa	GTEx
rs9934440	ACD	cis	parietal	SCAN
rs9934440	RP11-296I10.6	cis	Heart Left Ventricle	GTEx
rs9934440	EXOSC6	cis	Muscle Skeletal	GTEx
rs9934440	EXOSC6	Cis_1M	lymphoblastoid	RTeQTL
rs9934440	RP11-296I10.6	cis	Thyroid	GTEx
rs9934440	EXOSC6	cis	lung	GTEx
rs9934440	EXOSC6	cis	Heart Left Ventricle	GTEx
rs9934440	RP11-296I10.6	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70415800-70442000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr16:70422800-70441400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr16:70422800-70441600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr16:70428400-70442200	Weak transcription	Fetal Brain Male	brain
5	chr16:70428800-70450400	Weak transcription	Fetal Kidney	kidney
6	chr16:70431200-70441800	Weak transcription	Fetal Heart	heart
7	chr16:70432400-70444800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr16:70432800-70454800	Weak transcription	Pancreas	Pancrea
9	chr16:70432800-70457000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr16:70433200-70441400	Weak transcription	Brain Anterior Caudate	brain
11	chr16:70433200-70441400	Weak transcription	Ovary	ovary
12	chr16:70433200-70441800	Weak transcription	Brain Angular Gyrus	brain
13	chr16:70433200-70461600	Weak transcription	Aorta	Aorta
14	chr16:70433400-70441200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr16:70433400-70461600	Weak transcription	Brain Substantia Nigra	brain
16	chr16:70433600-70461600	Weak transcription	Colon Smooth Muscle	Colon
17	chr16:70433800-70441600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr16:70434200-70441600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr16:70434400-70441400	Weak transcription	Esophagus	oesophagus
20	chr16:70434400-70441600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr16:70434400-70448000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr16:70434600-70441400	Weak transcription	Gastric	stomach
23	chr16:70434600-70441600	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr16:70434600-70441600	Weak transcription	Brain Hippocampus Middle	brain
25	chr16:70434600-70444800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr16:70434800-70441800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr16:70434800-70441800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr16:70435000-70441400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr16:70435000-70441600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr16:70435000-70441600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr16:70435000-70451400	Weak transcription	Fetal Brain Female	brain
32	chr16:70435200-70441400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr16:70435200-70441400	Weak transcription	Brain Germinal Matrix	brain
34	chr16:70435200-70441800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr16:70435400-70441400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr16:70435400-70441400	Weak transcription	Right Ventricle	heart
37	chr16:70435600-70440600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr16:70435600-70441400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr16:70435600-70441400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr16:70436200-70439600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr16:70436400-70439200	Enhancers	Hela-S3	cervix
42	chr16:70436400-70439800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr16:70436400-70440200	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr16:70436600-70440400	Enhancers	Placenta	Placenta
45	chr16:70436800-70439200	Enhancers	HMEC	breast
46	chr16:70436800-70439600	Enhancers	Primary hematopoietic stem cells	blood
47	chr16:70437000-70439200	Enhancers	Thymus	Thymus
48	chr16:70437000-70439200	Enhancers	NHEK	skin
49	chr16:70437000-70439600	Enhancers	Fetal Thymus	thymus
50	chr16:70437000-70439800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links