Variant report

Variant	rs604369
Chromosome Location	chr1:10567208-10567209
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10567095..10568153-chr1:10926865..10927880,8	K562	blood:
2	chr1:10566900..10569422-chr1:10571271..10572995,2	K562	blood:
3	chr1:10488255..10489166-chr1:10567048..10567550,2	MCF-7	breast:
4	chr1:10566397..10569050-chr1:10569611..10571606,2	MCF-7	breast:
5	chr1:10566008..10570273-chr1:10573569..10578315,6	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10779737	0.88[EUR][1000 genomes]
rs11121579	0.81[CEU][hapmap]
rs11121581	0.96[EUR][1000 genomes]
rs11580264	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11584327	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12073943	0.89[EUR][1000 genomes]
rs12117392	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs12120962	1.00[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs12127400	1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap]
rs12565133	0.86[TSI][hapmap]
rs17035189	0.88[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs1755592	0.90[EUR][1000 genomes]
rs2186949	0.85[EUR][1000 genomes]
rs2274985	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2781233	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs589151	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602601	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs604814	0.96[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs6688558	1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap]
rs670666	0.81[ASW][hapmap];0.81[CEU][hapmap];0.89[TSI][hapmap]
rs684016	0.84[TSI][hapmap]
rs7419116	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7512495	0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs7543322	0.88[CEU][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7548453	0.88[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs7555790	1.00[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv2521	chr1:10553530-10598171	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs604369	APITD1	cis	cerebellum	SCAN
rs604369	PLEKHG5	cis	parietal	SCAN
rs604369	KIAA2013	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10554800-10568600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:10555200-10567400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:10555200-10567400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:10555200-10567400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:10555200-10568400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:10555200-10568600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:10555200-10570000	Weak transcription	Aorta	Aorta
8	chr1:10555400-10567400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:10555600-10567400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:10555600-10567400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:10555600-10567400	Weak transcription	A549	lung
12	chr1:10555600-10567600	Weak transcription	NH-A	brain
13	chr1:10555600-10567800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr1:10555600-10567800	Weak transcription	HSMM	muscle
15	chr1:10555600-10567800	Weak transcription	NHDF-Ad	bronchial
16	chr1:10555600-10568600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:10555600-10568600	Weak transcription	Pancreas	Pancrea
18	chr1:10555600-10568600	Weak transcription	HSMMtube	muscle
19	chr1:10555600-10570400	Weak transcription	Brain Substantia Nigra	brain
20	chr1:10555600-10570400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:10555600-10570600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:10555800-10567400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:10555800-10567400	Weak transcription	Osteobl	bone
24	chr1:10555800-10567800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:10555800-10567800	Weak transcription	Fetal Lung	lung
26	chr1:10555800-10568600	Weak transcription	Esophagus	oesophagus
27	chr1:10555800-10569600	Weak transcription	Colonic Mucosa	Colon
28	chr1:10555800-10570400	Weak transcription	Brain Anterior Caudate	brain
29	chr1:10556000-10567400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr1:10556000-10569400	Weak transcription	Fetal Brain Female	brain
31	chr1:10556000-10570200	Weak transcription	Brain Angular Gyrus	brain
32	chr1:10556400-10567400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:10556400-10567800	Weak transcription	Hela-S3	cervix
34	chr1:10556400-10570200	Weak transcription	Fetal Kidney	kidney
35	chr1:10556600-10568000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:10556600-10568600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:10556600-10570000	Weak transcription	Right Ventricle	heart
38	chr1:10556600-10570400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr1:10556600-10570400	Weak transcription	Stomach Mucosa	stomach
40	chr1:10556800-10567400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:10556800-10567600	Weak transcription	Primary T cells from cord blood	blood
42	chr1:10556800-10567800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:10556800-10567800	Weak transcription	Colon Smooth Muscle	Colon
44	chr1:10557000-10569600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:10557400-10568600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:10557600-10567400	Weak transcription	Fetal Muscle Leg	muscle
47	chr1:10557600-10567400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr1:10557600-10567600	Weak transcription	Fetal Muscle Trunk	muscle
49	chr1:10557600-10567600	Weak transcription	Fetal Stomach	stomach
50	chr1:10557600-10567800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links