Variant report

Variant	rs7668529
Chromosome Location	chr4:48349690-48349691
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48342295..48345695-chr4:48348596..48352687,7	MCF-7	breast:
2	chr4:48342958..48345732-chr4:48348835..48351792,2	MCF-7	breast:
3	chr4:48337400..48346343-chr4:48347805..48355704,14	K562	blood:
4	chr4:48348136..48350109-chr4:48359251..48361101,2	K562	blood:

Variant related genes	Relation type
ENSG00000109171	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10003230	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10026398	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10029785	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1117010	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12507206	0.81[EUR][1000 genomes]
rs12511991	0.81[EUR][1000 genomes]
rs12645951	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12649527	0.83[EUR][1000 genomes]
rs12649528	0.83[EUR][1000 genomes]
rs13105385	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13115295	0.81[EUR][1000 genomes]
rs13148849	0.81[EUR][1000 genomes]
rs13150017	0.80[EUR][1000 genomes]
rs1352433	0.82[EUR][1000 genomes]
rs1472967	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1586540	0.80[ASN][1000 genomes]
rs1703973	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1948167	0.80[ASN][1000 genomes]
rs2029348	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2291474	0.81[EUR][1000 genomes]
rs2291475	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2353312	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28409655	0.82[EUR][1000 genomes]
rs35758434	0.80[ASN][1000 genomes]
rs372825	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs382335	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3828496	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs392187	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs403495	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs404348	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs404445	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs404656	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs411261	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs421336	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs421833	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs429969	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs432927	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs445892	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs449376	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs450498	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4694895	0.80[ASN][1000 genomes]
rs62309425	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6447634	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6447635	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6816010	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6816352	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6821277	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6829705	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6836010	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6837335	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6844211	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6848073	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6848395	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7438704	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7672892	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7674269	0.81[EUR][1000 genomes]
rs7678164	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7700018	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs923372	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs923373	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9291323	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs974014	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs974015	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs974016	0.82[EUR][1000 genomes]
rs9996532	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[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	nsv1006610	chr4:48209294-48415387	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv537085	chr4:48209294-48415387	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7668529	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48344800-48352200	Weak transcription	Pancreas	Pancrea
2	chr4:48344800-48354400	Weak transcription	Esophagus	oesophagus
3	chr4:48344800-48362400	Weak transcription	Gastric	stomach
4	chr4:48345000-48350000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr4:48345400-48350400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:48345800-48353600	Weak transcription	Spleen	Spleen
7	chr4:48345800-48356000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:48345800-48356600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr4:48346000-48350000	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr4:48346000-48350800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:48346000-48351200	Weak transcription	A549	lung
12	chr4:48346000-48353000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr4:48346000-48362800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr4:48346200-48350600	Weak transcription	Brain Anterior Caudate	brain
15	chr4:48346200-48352200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr4:48346200-48354600	Weak transcription	Fetal Intestine Small	intestine
17	chr4:48346200-48356200	Weak transcription	Fetal Thymus	thymus
18	chr4:48346200-48356600	Weak transcription	HUVEC	blood vessel
19	chr4:48346200-48358400	Weak transcription	Small Intestine	intestine
20	chr4:48346200-48362400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:48346400-48350200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr4:48346400-48361200	Weak transcription	Thymus	Thymus
23	chr4:48346600-48350000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:48346600-48354800	Weak transcription	Primary B cells from cord blood	blood
25	chr4:48346600-48371000	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr4:48347000-48352200	Enhancers	Primary T cells from cord blood	blood
27	chr4:48347000-48354600	Weak transcription	Aorta	Aorta
28	chr4:48347200-48359600	Weak transcription	Fetal Stomach	stomach
29	chr4:48347400-48350800	Weak transcription	Fetal Brain Male	brain
30	chr4:48347400-48352200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr4:48347400-48353600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr4:48347400-48353800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr4:48347400-48354600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:48347400-48362200	Weak transcription	Brain Substantia Nigra	brain
35	chr4:48347400-48362200	Weak transcription	NHLF	lung
36	chr4:48347600-48349800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr4:48347600-48349800	Weak transcription	Liver	Liver
38	chr4:48347600-48350000	Weak transcription	Brain Hippocampus Middle	brain
39	chr4:48347600-48351200	Weak transcription	Brain Angular Gyrus	brain
40	chr4:48347600-48351800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr4:48347600-48351800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr4:48347600-48352800	Weak transcription	Fetal Kidney	kidney
43	chr4:48347600-48353000	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr4:48347600-48354600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr4:48347600-48365000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr4:48348200-48350800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:48348200-48353600	Weak transcription	Dnd41	blood
48	chr4:48348400-48352000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr4:48348600-48349800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr4:48348600-48350600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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