Variant report

Variant	rs6668967
Chromosome Location	chr1:228438900-228438901
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10737429	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10916292	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10916293	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150909	0.92[CEU][hapmap];0.83[GIH][hapmap]
rs1150912	0.89[CEU][hapmap]
rs1188704	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1188721	0.92[CEU][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs1188722	0.82[EUR][1000 genomes]
rs1188724	0.82[EUR][1000 genomes]
rs1188729	0.92[CEU][hapmap]
rs12022917	0.86[CHB][hapmap]
rs12035900	0.96[CEU][hapmap]
rs12741048	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12755546	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1411912	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1411915	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1757130	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1771455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1771456	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1771457	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1888680	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1888681	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs207951	0.91[CEU][hapmap]
rs2150669	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2487384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287613	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs369252	0.91[CEU][hapmap]
rs373610	0.91[CEU][hapmap];0.83[GIH][hapmap]
rs378090	0.92[CEU][hapmap];0.83[GIH][hapmap]
rs3795780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4085473	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs419338	0.92[CEU][hapmap]
rs450088	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4653932	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs533738	0.92[CEU][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs562634	0.91[CEU][hapmap]
rs564636	0.92[CEU][hapmap];0.83[GIH][hapmap]
rs6426493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426494	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6426495	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6426496	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6665929	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6677503	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517088	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517108	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7526808	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529241	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7532144	0.95[CEU][hapmap];0.84[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535667	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs867599	0.87[CEU][hapmap];0.87[GIH][hapmap];0.84[LWK][hapmap];0.87[TSI][hapmap];0.80[YRI][hapmap]
rs878388	0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs883749	0.96[CEU][hapmap]
rs936885	0.81[EUR][1000 genomes]
rs947084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
7	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
8	nsv1012078	chr1:228340876-228521843	Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
9	nsv535320	chr1:228340876-228521843	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
10	nsv873263	chr1:228391808-228494790	Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	nsv873264	chr1:228423647-228543800	Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv520340	chr1:228423936-228456147	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
13	nsv873265	chr1:228434395-228525008	Active TSS Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	nsv873266	chr1:228434395-228537942	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
15	nsv873267	chr1:228434395-228585837	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6668967	DUSP5P	cis	parietal	SCAN
rs6668967	C1orf69	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228429000-228439400	Strong transcription	HSMMtube	muscle
2	chr1:228430600-228447000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr1:228430800-228440000	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:228431200-228439800	Strong transcription	Left Ventricle	heart
5	chr1:228433200-228442400	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:228433400-228449400	Weak transcription	Brain Anterior Caudate	brain
7	chr1:228434000-228439600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:228434400-228440200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:228434400-228440400	Strong transcription	Fetal Muscle Trunk	muscle
10	chr1:228434400-228441600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:228434600-228439800	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr1:228434600-228439800	Weak transcription	Right Atrium	heart
13	chr1:228434600-228440200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:228434600-228440200	Strong transcription	Fetal Thymus	thymus
15	chr1:228434600-228440600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:228434600-228444400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:228434600-228455400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:228434800-228439200	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr1:228434800-228440600	Strong transcription	Fetal Stomach	stomach
20	chr1:228434800-228444000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:228434800-228444000	Weak transcription	Ovary	ovary
22	chr1:228434800-228444600	Strong transcription	Dnd41	blood
23	chr1:228434800-228445800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr1:228434800-228460000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:228434800-228462400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:228435000-228440400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr1:228435000-228441000	Strong transcription	Fetal Muscle Leg	muscle
28	chr1:228435000-228441200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:228435000-228441200	Weak transcription	Fetal Brain Male	brain
30	chr1:228435000-228442400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr1:228435000-228442800	Weak transcription	Aorta	Aorta
32	chr1:228435000-228444000	Weak transcription	Esophagus	oesophagus
33	chr1:228435000-228446000	Weak transcription	A549	lung
34	chr1:228435200-228440400	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:228435200-228440400	Strong transcription	Thymus	Thymus
36	chr1:228435200-228443200	Weak transcription	Fetal Kidney	kidney
37	chr1:228435200-228449400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:228435200-228449600	Strong transcription	Primary T cells from cord blood	blood
39	chr1:228435200-228462800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr1:228435400-228441800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:228435600-228439000	Weak transcription	Brain Germinal Matrix	brain
42	chr1:228435600-228462600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr1:228435800-228440000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:228435800-228446400	Weak transcription	Fetal Heart	heart
45	chr1:228435800-228450200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr1:228436000-228441200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:228436400-228439000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:228436400-228439600	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr1:228436600-228440200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr1:228436600-228440600	Strong transcription	Fetal Intestine Small	intestine

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