Variant report

Variant	rs636578
Chromosome Location	chr10:5938544-5938545
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:5936436..5938836-chr10:5955109..5956936,2	K562	blood:
2	chr10:5935432..5937214-chr10:5937982..5940044,2	MCF-7	breast:
3	chr10:5911390..5913912-chr10:5936445..5939123,2	MCF-7	breast:
4	chr10:5936708..5939190-chr10:5963280..5964936,2	MCF-7	breast:
5	chr10:5734425..5736308-chr10:5936922..5938867,2	K562	blood:
6	chr10:5936753..5940088-chr10:5944945..5949348,3	MCF-7	breast:
7	chr10:5852308..5856409-chr10:5935538..5939554,4	K562	blood:

Variant related genes	Relation type
ENSG00000108021	Chromatin interaction
ENSG00000057608	Chromatin interaction
ENSG00000272764	Chromatin interaction
ENSG00000134452	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs2274029	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap]
rs2320	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap]
rs2669122	0.97[ASN][1000 genomes]
rs2669126	0.93[ASN][1000 genomes]
rs4293039	0.84[CHB][hapmap]
rs582359	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.97[ASN][1000 genomes]
rs591510	0.88[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.96[ASN][1000 genomes]
rs591878	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs593610	0.86[CEU][hapmap];1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs595923	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.96[ASN][1000 genomes]
rs598331	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs603780	0.94[ASN][1000 genomes]
rs607728	0.94[ASN][1000 genomes]
rs610093	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs621628	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs622758	0.93[ASN][1000 genomes]
rs626344	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs633797	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs633928	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs633930	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs635532	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs647945	0.88[ASN][1000 genomes]
rs649537	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs664603	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs668498	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs670856	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs672126	0.90[ASN][1000 genomes]
rs680020	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs685852	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs686854	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs688388	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs792348	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs907687	0.84[CHB][hapmap]
rs980230	0.84[CHB][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	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv831775	chr10:5804335-6000849	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv825229	chr10:5886905-5967697	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv466724	chr10:5920836-5938544	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
7	nsv549906	chr10:5920836-5938544	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs636578	ANKRD16	cis	cerebellum	SCAN
rs636578	ANKRD16	cis	parietal	SCAN
rs636578	AKR1C2	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5933200-5948200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr10:5933200-5949800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr10:5933200-5977000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr10:5933400-5938800	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr10:5933400-5948200	Weak transcription	Ovary	ovary
6	chr10:5933400-5948400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr10:5933400-5949800	Weak transcription	Fetal Brain Male	brain
8	chr10:5933600-5948200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr10:5933600-5951600	Weak transcription	Stomach Mucosa	stomach
10	chr10:5933800-5939200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr10:5933800-5941200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr10:5934000-5939800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr10:5934200-5938600	Strong transcription	Fetal Intestine Large	intestine
14	chr10:5934200-5939400	Strong transcription	Fetal Muscle Leg	muscle
15	chr10:5934600-5941000	Strong transcription	NHEK	skin
16	chr10:5934800-5940200	Weak transcription	Colon Smooth Muscle	Colon
17	chr10:5934800-5948000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr10:5935200-5941800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr10:5935200-5947400	Weak transcription	Small Intestine	intestine
20	chr10:5935400-5938600	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr10:5935400-5939200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr10:5935400-5939800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr10:5935400-5940400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr10:5935400-5941200	Strong transcription	Fetal Lung	lung
25	chr10:5935600-5938600	Strong transcription	Primary hematopoietic stem cells	blood
26	chr10:5935600-5939000	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr10:5935600-5939400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr10:5935600-5940200	Strong transcription	Placenta	Placenta
29	chr10:5935600-5943000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr10:5935600-5962000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr10:5935800-5939000	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr10:5935800-5939200	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr10:5935800-5939400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr10:5935800-5940400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr10:5935800-5940400	Strong transcription	Osteobl	bone
36	chr10:5936000-5938600	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr10:5936000-5938600	Genic enhancers	Left Ventricle	heart
38	chr10:5936000-5938800	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr10:5936000-5938800	Strong transcription	NHDF-Ad	bronchial
40	chr10:5936000-5939000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr10:5936000-5939200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
42	chr10:5936000-5939400	Genic enhancers	Primary T cells from cord blood	blood
43	chr10:5936000-5939400	Strong transcription	Esophagus	oesophagus
44	chr10:5936000-5939400	Strong transcription	Fetal Intestine Small	intestine
45	chr10:5936000-5939600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr10:5936000-5939600	Strong transcription	Stomach Smooth Muscle	stomach
47	chr10:5936000-5939600	Strong transcription	NHLF	lung
48	chr10:5936000-5940000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr10:5936000-5940000	Strong transcription	Adipose Nuclei	Adipose
50	chr10:5936000-5940000	Strong transcription	Fetal Stomach	stomach

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