Variant report

Variant	rs12244472
Chromosome Location	chr10:52175079-52175080
allele	A/G
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:52160595..52164108-chr10:52172645..52175372,3	MCF-7	breast:
2	chr10:52173595..52180106-chr10:52381535..52385847,7	MCF-7	breast:
3	chr10:52173619..52179913-chr10:52381938..52386991,6	K562	blood:
4	chr10:52152378..52155454-chr10:52174313..52178963,4	MCF-7	breast:
5	chr10:52164630..52167501-chr10:52173843..52176462,2	MCF-7	breast:
6	chr10:52173349..52175159-chr10:52175578..52178225,2	K562	blood:
7	chr10:52152624..52157680-chr10:52173844..52179255,6	K562	blood:
8	chr10:52136978..52138506-chr10:52174976..52177884,2	K562	blood:
9	chr10:52084222..52086810-chr10:52173871..52176505,2	K562	blood:
10	chr10:52164112..52165618-chr10:52174506..52177347,2	K562	blood:
11	chr10:52174976..52177960-chr10:52379518..52382234,2	K562	blood:

No data

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

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10159614	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10825837	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10825903	0.97[ASN][1000 genomes]
rs11005454	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11005521	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11005612	0.97[ASN][1000 genomes]
rs11005901	1.00[AMR][1000 genomes]
rs11005920	1.00[AMR][1000 genomes]
rs11006017	1.00[AMR][1000 genomes]
rs11815109	1.00[AMR][1000 genomes]
rs12245709	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12246357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12251096	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12252248	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12252843	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12253726	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12253887	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12255967	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12262002	1.00[AMR][1000 genomes]
rs12262586	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12265260	0.90[ASN][1000 genomes]
rs12265364	1.00[AMR][1000 genomes]
rs56208258	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57325762	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59725568	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61152656	1.00[AMR][1000 genomes]
rs7073693	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7077375	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7084809	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7097717	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7097865	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73316672	1.00[AMR][1000 genomes]
rs73316673	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73316690	1.00[AMR][1000 genomes]
rs73330990	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73332908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73332909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74132707	0.97[ASN][1000 genomes]
rs7916018	1.00[AMR][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:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52147000-52176600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr10:52157200-52177600	Weak transcription	Spleen	Spleen
3	chr10:52157800-52175400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr10:52157800-52176800	Weak transcription	Lung	lung
5	chr10:52160800-52176800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr10:52163600-52176800	Weak transcription	Thymus	Thymus
7	chr10:52164400-52177600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr10:52164600-52176600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr10:52166600-52175800	Weak transcription	Primary T cells from cord blood	blood
10	chr10:52166600-52177400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr10:52166800-52177200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr10:52166800-52177400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr10:52167000-52176800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr10:52167000-52176800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr10:52167000-52177200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr10:52167000-52177400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr10:52167600-52176800	Weak transcription	Primary B cells from cord blood	blood
18	chr10:52168000-52177400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr10:52168600-52176200	Weak transcription	Right Atrium	heart
20	chr10:52168600-52176600	Weak transcription	Fetal Brain Male	brain
21	chr10:52170200-52176400	Weak transcription	Small Intestine	intestine
22	chr10:52170200-52176800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr10:52170400-52175200	Enhancers	Hela-S3	cervix
24	chr10:52170400-52176200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr10:52170400-52176800	Weak transcription	Right Ventricle	heart
26	chr10:52170400-52178400	Active TSS	GM12878-XiMat	blood
27	chr10:52170600-52175200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr10:52170600-52175200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr10:52170600-52175600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr10:52170600-52176200	Weak transcription	HMEC	breast
31	chr10:52170600-52176600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr10:52170600-52176600	Weak transcription	NH-A	brain
33	chr10:52170600-52176800	Weak transcription	Aorta	Aorta
34	chr10:52170600-52177400	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr10:52170600-52177400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr10:52170600-52177600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr10:52170800-52176400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr10:52171200-52175200	Weak transcription	HSMM	muscle
39	chr10:52171400-52175400	Weak transcription	NHEK	skin
40	chr10:52171400-52175400	Weak transcription	NHLF	lung
41	chr10:52171400-52176000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr10:52171400-52176000	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr10:52171400-52176800	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr10:52171600-52176200	Weak transcription	HUVEC	blood vessel
45	chr10:52171600-52176200	Weak transcription	Osteobl	bone
46	chr10:52171800-52175200	Enhancers	Liver	Liver
47	chr10:52171800-52176800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr10:52172000-52175200	Weak transcription	Pancreas	Pancrea
49	chr10:52172000-52175600	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr10:52172000-52176000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links