Variant report

Variant	rs597441
Chromosome Location	chr1:10493415-10493416
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	WRNIP1	chr1:10493298-10493883	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:10490607..10494447-chr1:10532445..10535163,5	K562	blood:
2	chr1:10489448..10493967-chr1:10494423..10498103,7	K562	blood:
3	chr1:10457881..10459696-chr1:10491385..10493588,2	MCF-7	breast:

Variant related genes	Relation type
APITD1-CORT	TF binding region
ENSG00000271989	TF binding region
ENSG00000251503	Chromatin interaction
ENSG00000142655	Chromatin interaction
ENSG00000142657	Chromatin interaction
ENSG00000160049	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10436981	0.81[EUR][1000 genomes]
rs11121579	0.92[CEU][hapmap]
rs12565133	0.89[CEU][hapmap]
rs1307485	0.96[CEU][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs1307487	0.82[EUR][1000 genomes]
rs1760664	0.83[EUR][1000 genomes]
rs2483679	0.80[MEX][hapmap]
rs2483684	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2781233	0.92[CEU][hapmap];0.81[GIH][hapmap]
rs35138970	0.81[EUR][1000 genomes]
rs3828044	0.82[TSI][hapmap]
rs475549	0.84[EUR][1000 genomes]
rs481571	0.96[CEU][hapmap];0.89[GIH][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs491880	0.96[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs505141	0.96[CEU][hapmap];0.89[GIH][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs519472	0.85[EUR][1000 genomes]
rs520964	0.82[EUR][1000 genomes]
rs522029	0.84[EUR][1000 genomes]
rs522280	0.85[EUR][1000 genomes]
rs524150	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs528713	0.96[CEU][hapmap];0.89[GIH][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs583515	0.82[EUR][1000 genomes]
rs586223	0.92[CEU][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs628462	0.81[CHB][hapmap]
rs632690	0.81[EUR][1000 genomes]
rs634358	0.96[CEU][hapmap];0.81[GIH][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs649101	0.92[CEU][hapmap];0.89[GIH][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs649639	0.85[EUR][1000 genomes]
rs6662684	0.81[EUR][1000 genomes]
rs666583	0.83[EUR][1000 genomes]
rs670666	0.92[CEU][hapmap]
rs673254	0.92[CEU][hapmap]
rs678850	0.85[EUR][1000 genomes]
rs681448	0.82[EUR][1000 genomes]
rs684016	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[GIH][hapmap];0.84[MEX][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
rs597441	PLEKHG5	cis	parietal	SCAN
rs597441	APITD1	cis	cerebellum	SCAN
rs597441	NPPA	cis	cerebellum	SCAN
rs597441	KIAA2013	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10491400-10493600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:10491400-10504600	Weak transcription	Lung	lung
3	chr1:10491400-10519000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:10491400-10521000	Weak transcription	Ovary	ovary
5	chr1:10491400-10521200	Weak transcription	Aorta	Aorta
6	chr1:10491600-10494000	Weak transcription	Fetal Kidney	kidney
7	chr1:10491600-10496800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:10491600-10500000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:10491600-10500400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:10491600-10504600	Weak transcription	HSMMtube	muscle
11	chr1:10491600-10508000	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:10491600-10510200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:10491600-10510200	Weak transcription	Gastric	stomach
14	chr1:10491600-10510400	Weak transcription	Right Atrium	heart
15	chr1:10491600-10511000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr1:10491600-10511000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:10491600-10511200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:10491600-10516200	Weak transcription	HMEC	breast
19	chr1:10491600-10517800	Weak transcription	Primary T cells from cord blood	blood
20	chr1:10491600-10518000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:10491600-10518000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:10491600-10519200	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr1:10491600-10521200	Weak transcription	Brain Substantia Nigra	brain
24	chr1:10491600-10521200	Weak transcription	Left Ventricle	heart
25	chr1:10491600-10521200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr1:10491600-10521200	Weak transcription	Spleen	Spleen
27	chr1:10491600-10521400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:10491800-10493800	Enhancers	Duodenum Mucosa	Duodenum
29	chr1:10491800-10494200	Enhancers	Fetal Intestine Large	intestine
30	chr1:10491800-10494200	Enhancers	Pancreas	Pancrea
31	chr1:10491800-10494200	Enhancers	HepG2	liver
32	chr1:10491800-10494600	Weak transcription	Placenta	Placenta
33	chr1:10491800-10494800	Weak transcription	Fetal Muscle Leg	muscle
34	chr1:10491800-10495000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:10491800-10495000	Weak transcription	Fetal Stomach	stomach
36	chr1:10491800-10495800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr1:10491800-10497000	Weak transcription	Right Ventricle	heart
38	chr1:10491800-10497800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr1:10491800-10498400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:10491800-10498600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:10491800-10500800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:10491800-10501000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:10491800-10504400	Weak transcription	Adipose Nuclei	Adipose
44	chr1:10491800-10504400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr1:10491800-10508400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr1:10491800-10508800	Weak transcription	Colonic Mucosa	Colon
47	chr1:10491800-10509600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr1:10491800-10510000	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr1:10491800-10510200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr1:10491800-10510200	Weak transcription	Brain Anterior Caudate	brain

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