Variant report

Variant	rs6668685
Chromosome Location	chr1:92791812-92791813
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10747411	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10782838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10782922	0.94[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10874656	0.82[AMR][1000 genomes]
rs10875348	1.00[YRI][hapmap]
rs11166568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11166575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1226177	1.00[ASN][1000 genomes]
rs1226188	1.00[ASN][1000 genomes]
rs1234874	1.00[ASN][1000 genomes]
rs1386585	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1487537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1487539	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17131767	1.00[ASN][1000 genomes]
rs1748178	1.00[ASN][1000 genomes]
rs17519833	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17579779	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1825813	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1886682	0.94[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1886683	0.94[CEU][hapmap]
rs1906279	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2025607	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2046621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391139	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391140	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2763040	1.00[ASN][1000 genomes]
rs3103177	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3103180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3122320	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131815	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131816	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131831	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4247165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4375281	0.88[CEU][hapmap]
rs475034	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs476490	1.00[ASN][1000 genomes]
rs481384	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs481677	1.00[ASN][1000 genomes]
rs487443	1.00[ASN][1000 genomes]
rs495446	1.00[ASN][1000 genomes]
rs4970696	0.82[AMR][1000 genomes]
rs4970698	0.82[AMR][1000 genomes]
rs4970708	0.82[AMR][1000 genomes]
rs4970709	0.94[CEU][hapmap]
rs4970710	0.94[CEU][hapmap]
rs501872	1.00[ASN][1000 genomes]
rs510857	1.00[ASN][1000 genomes]
rs517404	1.00[ASN][1000 genomes]
rs523692	1.00[ASN][1000 genomes]
rs524989	1.00[ASN][1000 genomes]
rs525834	1.00[ASN][1000 genomes]
rs530815	1.00[ASN][1000 genomes]
rs532031	1.00[ASN][1000 genomes]
rs533124	1.00[ASN][1000 genomes]
rs533418	1.00[ASN][1000 genomes]
rs537754	1.00[ASN][1000 genomes]
rs538054	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs541168	1.00[ASN][1000 genomes]
rs544556	1.00[ASN][1000 genomes]
rs548100	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs548141	1.00[ASN][1000 genomes]
rs552468	1.00[ASN][1000 genomes]
rs553173	1.00[ASN][1000 genomes]
rs562119	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs564077	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs566576	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs579668	1.00[ASN][1000 genomes]
rs59679370	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6603963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6603967	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6603979	0.94[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6603984	0.80[AMR][1000 genomes]
rs6603985	0.82[AMR][1000 genomes]
rs6604089	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6676141	0.80[EUR][1000 genomes]
rs6686702	0.93[CEU][hapmap]
rs6692060	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512301	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518357	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7520275	1.00[CHB][hapmap]
rs7542747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545445	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547429	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7552212	0.81[EUR][1000 genomes]
rs912795	0.94[CEU][hapmap];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv530046	chr1:92277460-92799794	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv830592	chr1:92669282-92805629	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv870667	chr1:92697188-92813741	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv871352	chr1:92761127-92807238	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv870854	chr1:92765102-92807238	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv871387	chr1:92765102-92813741	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6668685	RPL5	cis	parietal	SCAN
rs6668685	FAM69A	cis	cerebellum	SCAN
rs6668685	RPL10A	trans	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92765200-92792000	Weak transcription	Aorta	Aorta
2	chr1:92765200-92792000	Weak transcription	Esophagus	oesophagus
3	chr1:92765600-92792000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:92765600-92792000	Weak transcription	Spleen	Spleen
5	chr1:92765800-92850000	Weak transcription	Small Intestine	intestine
6	chr1:92766000-92792000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:92771800-92794800	Weak transcription	Brain Angular Gyrus	brain
8	chr1:92771800-92823800	Weak transcription	Colonic Mucosa	Colon
9	chr1:92773000-92800800	Weak transcription	NHDF-Ad	bronchial
10	chr1:92778000-92799200	Weak transcription	Hela-S3	cervix
11	chr1:92781800-92792000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:92782200-92803400	Weak transcription	Stomach Mucosa	stomach
13	chr1:92784400-92808200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr1:92785000-92792000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr1:92785200-92793400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:92789000-92792000	Strong transcription	Fetal Intestine Large	intestine
17	chr1:92789000-92792200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:92789000-92792200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:92789000-92792400	Strong transcription	Osteobl	bone
20	chr1:92789000-92792600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:92789000-92792600	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr1:92789200-92792400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:92789600-92792000	Weak transcription	Colon Smooth Muscle	Colon
24	chr1:92789600-92796000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:92789800-92792200	Weak transcription	Fetal Heart	heart
26	chr1:92789800-92792400	Strong transcription	Primary T cells from cord blood	blood
27	chr1:92789800-92812000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:92789800-92830600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr1:92790000-92794400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr1:92790000-92815200	Weak transcription	Psoas Muscle	Psoas
31	chr1:92790400-92792000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr1:92790400-92792000	Weak transcription	NH-A	brain
33	chr1:92790400-92794600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:92790400-92797800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr1:92790400-92803600	Weak transcription	HUVEC	blood vessel
36	chr1:92790600-92792800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:92790600-92793600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
38	chr1:92790800-92793400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
39	chr1:92790800-92802200	Weak transcription	HepG2	liver
40	chr1:92791000-92792600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
41	chr1:92791000-92793200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr1:92791200-92792000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
43	chr1:92791200-92792000	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr1:92791200-92792000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr1:92791200-92792400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
46	chr1:92791200-92792400	ZNF genes & repeats	K562	blood
47	chr1:92791200-92793600	ZNF genes & repeats	Dnd41	blood
48	chr1:92791200-92793800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:92791200-92795800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
50	chr1:92791400-92792000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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