Variant report

Variant	rs670666
Chromosome Location	chr1:10549380-10549381
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:10534437..10535976-chr1:10547200..10549978,2	K562	blood:
2	chr1:10548374..10550861-chr1:10557856..10560546,2	K562	blood:

Variant related genes	Relation type
ENSG00000142655	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10746494	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11121579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11584327	0.81[ASW][hapmap];0.81[CEU][hapmap];0.89[TSI][hapmap]
rs1203122	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12073943	0.85[EUR][1000 genomes]
rs12565133	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1307485	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1307487	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17035189	0.84[CEU][hapmap];0.87[TSI][hapmap]
rs1750349	0.83[ASN][1000 genomes]
rs1755592	0.82[EUR][1000 genomes]
rs1760664	0.84[ASN][1000 genomes]
rs2186949	0.90[EUR][1000 genomes]
rs2274985	0.81[ASW][hapmap];0.81[CEU][hapmap];0.89[TSI][hapmap]
rs2483679	0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs2483684	0.83[ASN][1000 genomes]
rs2781233	0.81[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs481571	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs491880	0.96[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs505141	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs528713	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs585406	0.84[EUR][1000 genomes]
rs586223	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap]
rs597441	0.92[CEU][hapmap]
rs604369	0.81[ASW][hapmap];0.81[CEU][hapmap];0.89[TSI][hapmap]
rs604814	0.82[TSI][hapmap]
rs628462	0.90[CHB][hapmap];0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs634358	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs649101	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs655271	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs663864	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs672606	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs673254	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs684016	0.96[CEU][hapmap];0.81[CHD][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs685746	0.81[YRI][hapmap]
rs7419116	0.81[CEU][hapmap]
rs7543322	0.84[TSI][hapmap]
rs7548453	0.84[CEU][hapmap];0.89[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs670666	APITD1	cis	cerebellum	SCAN
rs670666	PEX14	cis	multi-tissue	Pritchard
rs670666	PLEKHG5	cis	parietal	SCAN
rs670666	KIAA2013	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10535800-10555000	Weak transcription	Aorta	Aorta
2	chr1:10536000-10549800	Weak transcription	Gastric	stomach
3	chr1:10536000-10549800	Weak transcription	Left Ventricle	heart
4	chr1:10536000-10550200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:10536000-10555000	Weak transcription	Esophagus	oesophagus
6	chr1:10536000-10555000	Weak transcription	HSMMtube	muscle
7	chr1:10536000-10555600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:10536200-10555000	Weak transcription	NH-A	brain
9	chr1:10536400-10549400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr1:10536400-10549400	Weak transcription	A549	lung
11	chr1:10536400-10549600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:10536400-10549800	Weak transcription	Primary B cells from cord blood	blood
13	chr1:10536400-10550000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:10536400-10550000	Weak transcription	Brain Germinal Matrix	brain
15	chr1:10536400-10553000	Weak transcription	Psoas Muscle	Psoas
16	chr1:10536400-10554000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:10536400-10554600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:10536400-10554800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr1:10536400-10554800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:10536400-10554800	Weak transcription	Fetal Brain Male	brain
21	chr1:10536400-10554800	Weak transcription	NHDF-Ad	bronchial
22	chr1:10536400-10555000	Weak transcription	Fetal Kidney	kidney
23	chr1:10536400-10555000	Weak transcription	HSMM	muscle
24	chr1:10536600-10549400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:10536600-10549400	Weak transcription	Primary B cells from peripheral blood	blood
26	chr1:10536600-10549400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr1:10536600-10549400	Weak transcription	Fetal Lung	lung
28	chr1:10536600-10549400	Weak transcription	GM12878-XiMat	blood
29	chr1:10536600-10549400	Weak transcription	Hela-S3	cervix
30	chr1:10536600-10549600	Weak transcription	Brain Hippocampus Middle	brain
31	chr1:10536600-10549800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:10536600-10550000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr1:10536600-10550000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:10536600-10550200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:10536600-10550200	Weak transcription	Brain Anterior Caudate	brain
36	chr1:10536600-10554800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:10536600-10555000	Weak transcription	Brain Substantia Nigra	brain
38	chr1:10536800-10549400	Weak transcription	Fetal Muscle Trunk	muscle
39	chr1:10536800-10549600	Weak transcription	Placenta	Placenta
40	chr1:10536800-10549800	Weak transcription	Fetal Brain Female	brain
41	chr1:10536800-10549800	Weak transcription	Right Ventricle	heart
42	chr1:10536800-10550000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:10536800-10554600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr1:10536800-10554600	Weak transcription	Pancreas	Pancrea
45	chr1:10536800-10554600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr1:10537000-10549400	Weak transcription	Fetal Thymus	thymus
47	chr1:10537000-10549400	Weak transcription	Small Intestine	intestine
48	chr1:10537000-10554600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:10537000-10554800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr1:10537000-10554800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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