Variant report

Variant	rs1203416
Chromosome Location	chr10:52176944-52176945
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:52176233..52179172-chr10:52229395..52232901,6	MCF-7	breast:
2	chr10:52176817..52177809-chr11:65271375..65272246,2	Hela-S3	cervix:
3	chr10:52176588..52178104-chr10:52321160..52323318,2	MCF-7	breast:
4	chr10:52173595..52180106-chr10:52381535..52385847,7	MCF-7	breast:
5	chr10:52173619..52179913-chr10:52381938..52386991,6	K562	blood:
6	chr10:52152378..52155454-chr10:52174313..52178963,4	MCF-7	breast:
7	chr10:52173349..52175159-chr10:52175578..52178225,2	K562	blood:
8	chr10:52176384..52177328-chr5:171741288..171742195,2	Hela-S3	cervix:
9	chr10:52152624..52157680-chr10:52173844..52179255,6	K562	blood:
10	chr10:52176732..52178529-chr10:52382760..52384432,2	MCF-7	breast:
11	chr10:52175389..52176966-chr10:52179598..52182050,2	K562	blood:
12	chr10:52136978..52138506-chr10:52174976..52177884,2	K562	blood:
13	chr10:52164112..52165618-chr10:52174506..52177347,2	K562	blood:
14	chr10:52174976..52177960-chr10:52379518..52382234,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000226200	Chromatin interaction
ENSG00000198964	Chromatin interaction
ENSG00000225303	Chromatin interaction
ENSG00000269700	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1203374	1.00[ASN][1000 genomes]
rs1203378	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1203379	1.00[ASN][1000 genomes]
rs1203383	1.00[ASN][1000 genomes]
rs1203384	1.00[ASN][1000 genomes]
rs1203391	1.00[ASN][1000 genomes]
rs1203402	1.00[ASN][1000 genomes]
rs1203412	1.00[ASN][1000 genomes]
rs1203417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203419	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203422	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203427	1.00[ASN][1000 genomes]
rs1211373	1.00[ASN][1000 genomes]
rs2024871	1.00[ASN][1000 genomes]
rs2208035	1.00[ASN][1000 genomes]
rs2474611	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2574945	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2574976	1.00[ASN][1000 genomes]
rs2688874	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688876	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688883	1.00[ASN][1000 genomes]
rs2688884	1.00[ASN][1000 genomes]
rs2842099	1.00[ASN][1000 genomes]
rs2842110	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983348	1.00[ASN][1000 genomes]
rs2983372	1.00[ASN][1000 genomes]
rs3011712	1.00[ASN][1000 genomes]
rs3011715	1.00[ASN][1000 genomes]
rs3011768	1.00[ASN][1000 genomes]
rs3011795	1.00[ASN][1000 genomes]
rs72801753	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7923756	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910819	1.00[ASN][1000 genomes]
rs9416590	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	nsv521273	chr10:52051645-52197847	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv948006	chr10:52127164-52177684	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52157200-52177600	Weak transcription	Spleen	Spleen
2	chr10:52164400-52177600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr10:52166600-52177400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr10:52166800-52177200	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr10:52166800-52177400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr10:52167000-52177200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr10:52167000-52177400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr10:52168000-52177400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr10:52170400-52178400	Active TSS	GM12878-XiMat	blood
10	chr10:52170600-52177400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr10:52170600-52177400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr10:52170600-52177600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr10:52172400-52177400	Weak transcription	Gastric	stomach
14	chr10:52173400-52177400	Weak transcription	Fetal Intestine Large	intestine
15	chr10:52173600-52177600	Weak transcription	Stomach Mucosa	stomach
16	chr10:52174200-52177200	Weak transcription	Psoas Muscle	Psoas
17	chr10:52174400-52177400	Enhancers	Fetal Heart	heart
18	chr10:52175200-52177800	Flanking Active TSS	Liver	Liver
19	chr10:52175600-52177200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr10:52175600-52177400	Active TSS	Duodenum Mucosa	Duodenum
21	chr10:52175600-52177400	Active TSS	Fetal Lung	lung
22	chr10:52175600-52177400	Weak transcription	Pancreas	Pancrea
23	chr10:52175600-52177400	Active TSS	NHLF	lung
24	chr10:52175600-52177600	Active TSS	K562	blood
25	chr10:52175600-52178400	Active TSS	Fetal Kidney	kidney
26	chr10:52175800-52177400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr10:52176000-52177000	Flanking Active TSS	NHEK	skin
28	chr10:52176000-52177200	Weak transcription	Primary T cells from cord blood	blood
29	chr10:52176000-52177400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr10:52176000-52177600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr10:52176000-52177600	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr10:52176000-52178400	Active TSS	Brain Cingulate Gyrus	brain
33	chr10:52176000-52178400	Active TSS	Placenta	Placenta
34	chr10:52176200-52177000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr10:52176200-52177000	Flanking Active TSS	A549	lung
36	chr10:52176200-52177200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr10:52176200-52177200	Enhancers	Osteobl	bone
38	chr10:52176200-52177600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr10:52176200-52177600	Flanking Active TSS	HUVEC	blood vessel
40	chr10:52176200-52178400	Active TSS	Hela-S3	cervix
41	chr10:52176200-52178800	Active TSS	Right Atrium	heart
42	chr10:52176200-52178800	Active TSS	NHDF-Ad	bronchial
43	chr10:52176400-52177000	Flanking Active TSS	HMEC	breast
44	chr10:52176400-52177200	Active TSS	Fetal Muscle Leg	muscle
45	chr10:52176400-52177600	Enhancers	Small Intestine	intestine
46	chr10:52176400-52178400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr10:52176400-52178800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr10:52176400-52178800	Active TSS	HSMMtube	muscle
49	chr10:52176600-52177000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr10:52176600-52177000	Flanking Active TSS	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links