Variant report

Variant	rs60177889
Chromosome Location	chr10:52389659-52389660
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr10:52389567-52389794	H1-hESC	embryonic stem cell:	n/a	n/a
2	SP1	chr10:52389471-52389835	H1-hESC	embryonic stem cell:	n/a	n/a
3	HDAC2	chr10:52389508-52389808	H1-hESC	embryonic stem cell:	n/a	n/a
4	GTF2F1	chr10:52389648-52389666	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr10:52389604-52389795	H1-hESC	embryonic stem cell:	n/a	n/a
6	SP1	chr10:52389590-52389866	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr10:52389607-52389815	H1-hESC	embryonic stem cell:	n/a	n/a
8	RAD21	chr10:52389506-52389850	H1-hESC	embryonic stem cell:	n/a	n/a
9	TCF12	chr10:52389639-52389837	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:52389046..52395992-chr10:52408718..52416095,10	K562	blood:
2	chr10:52385910..52390098-chr10:52396807..52399699,3	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ASAH2B-2	chr10:52389337-52391396	ENSG00000226200.1
2	lnc-ASAH2B-2	chr10:52389337-52401211	ENSG00000226200.2
3	lnc-ASAH2B-2	chr10:52389337-52389732	ENSG00000226200.2

No data

Variant related genes	Relation type
SGMS1	TF binding region
ENSG00000231345	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10826243	0.92[ASN][1000 genomes]
rs10826273	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006328	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006358	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006369	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006434	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11006441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11006474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11006476	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11006477	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11006479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006493	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12358192	0.92[ASN][1000 genomes]
rs12358348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12358866	0.92[ASN][1000 genomes]
rs12360512	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17581567	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17582633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55763387	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55953936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55969688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56029434	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56044934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56306926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57002092	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7904306	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52385400-52392400	Weak transcription	Lung	lung
2	chr10:52385600-52392200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr10:52385600-52392200	Weak transcription	Left Ventricle	heart
4	chr10:52385600-52392400	Weak transcription	Gastric	stomach
5	chr10:52385600-52393000	Weak transcription	Pancreas	Pancrea
6	chr10:52385600-52393600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr10:52385600-52395200	Weak transcription	Esophagus	oesophagus
8	chr10:52385800-52391000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr10:52385800-52391600	Weak transcription	Brain Angular Gyrus	brain
10	chr10:52385800-52392800	Weak transcription	Aorta	Aorta
11	chr10:52385800-52394800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr10:52385800-52395000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr10:52385800-52396000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr10:52385800-52396800	Weak transcription	Fetal Brain Male	brain
15	chr10:52385800-52397000	Weak transcription	Psoas Muscle	Psoas
16	chr10:52385800-52397000	Weak transcription	Small Intestine	intestine
17	chr10:52386000-52390000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr10:52386000-52390200	Weak transcription	NHEK	skin
19	chr10:52386000-52390400	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr10:52386000-52390600	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr10:52386000-52391600	Weak transcription	Fetal Kidney	kidney
22	chr10:52386000-52391600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr10:52386000-52392200	Weak transcription	Fetal Stomach	stomach
24	chr10:52386000-52392200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr10:52386000-52392400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr10:52386000-52392400	Weak transcription	Fetal Intestine Small	intestine
27	chr10:52386000-52393400	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr10:52386000-52394600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr10:52386000-52394800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr10:52386000-52394800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr10:52386000-52394800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr10:52386000-52394800	Weak transcription	HSMM	muscle
33	chr10:52386000-52395000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr10:52386000-52395200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr10:52386000-52395800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr10:52386000-52396000	Weak transcription	Primary hematopoietic stem cells	blood
37	chr10:52386000-52397000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr10:52386000-52400400	Weak transcription	Fetal Lung	lung
39	chr10:52386200-52390600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr10:52386200-52396200	Weak transcription	Primary B cells from cord blood	blood
41	chr10:52386200-52396200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr10:52386400-52393600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr10:52386800-52390800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr10:52387000-52390800	Strong transcription	Liver	Liver
45	chr10:52387200-52390600	Enhancers	H1 Cell Line	embryonic stem cell
46	chr10:52387200-52390800	Strong transcription	Primary B cells from peripheral blood	blood
47	chr10:52388200-52394600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr10:52388400-52390200	Strong transcription	Adipose Nuclei	Adipose
49	chr10:52388400-52394600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr10:52388600-52390200	Enhancers	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links