Variant report

Variant	rs12321910
Chromosome Location	chr12:50161734-50161735
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:50161173-50161787	MCF-7	breast:	n/a	n/a
2	POLR2A	chr12:50158575-50161824	U87	brain:	n/a	n/a
3	POLR2A	chr12:50158581-50161762	U87	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50156443..50162111-chr12:50232191..50236705,6	K562	blood:
2	chr12:50141439..50143610-chr12:50160538..50162943,2	MCF-7	breast:
3	chr12:50135671..50138899-chr12:50159080..50162022,3	K562	blood:
4	chr12:50156738..50159324-chr12:50159902..50162287,2	MCF-7	breast:
5	chr12:50143754..50145510-chr12:50159817..50162056,2	MCF-7	breast:
6	chr12:50156927..50158819-chr12:50161421..50163054,2	MCF-7	breast:
7	chr12:50159154..50162859-chr12:50163370..50168392,4	MCF-7	breast:

No data

Variant related genes	Relation type
LSM6P2	TF binding region
ENSG00000257730	Chromatin interaction
ENSG00000139644	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10160960	0.86[ASN][1000 genomes]
rs10161088	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10219602	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1049986	0.80[ASN][1000 genomes]
rs1078216	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169108	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169121	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169128	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169129	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169130	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169132	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11503899	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12304910	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12306114	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12306565	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12308256	0.80[ASN][1000 genomes]
rs12308567	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12309717	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12314676	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12315732	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12316284	0.80[ASN][1000 genomes]
rs12321935	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28654319	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28755804	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56784440	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57144906	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58250762	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59511398	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59811112	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60402517	0.81[ASN][1000 genomes]
rs7136772	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7136990	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73306854	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73306885	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73309015	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7688	0.80[ASN][1000 genomes]
rs7967624	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50148200-50170000	Weak transcription	Right Atrium	heart
2	chr12:50158200-50162600	Weak transcription	Fetal Heart	heart
3	chr12:50158200-50170200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr12:50158400-50161800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:50158400-50161800	Weak transcription	Psoas Muscle	Psoas
6	chr12:50158400-50161800	Weak transcription	Stomach Mucosa	stomach
7	chr12:50158400-50162600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:50158400-50163400	Weak transcription	Spleen	Spleen
9	chr12:50158400-50170000	Weak transcription	Esophagus	oesophagus
10	chr12:50158400-50170200	Weak transcription	A549	lung
11	chr12:50158400-50170200	Weak transcription	K562	blood
12	chr12:50158800-50163800	Weak transcription	GM12878-XiMat	blood
13	chr12:50158800-50170200	Weak transcription	Primary B cells from peripheral blood	blood
14	chr12:50158800-50170400	Weak transcription	Primary B cells from cord blood	blood
15	chr12:50158800-50181600	Weak transcription	Brain Hippocampus Middle	brain
16	chr12:50159000-50162200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr12:50159000-50162200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr12:50159000-50162600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:50159000-50163800	Weak transcription	Pancreas	Pancrea
20	chr12:50159000-50164200	Weak transcription	Dnd41	blood
21	chr12:50159000-50167600	Weak transcription	HSMMtube	muscle
22	chr12:50159000-50170000	Weak transcription	Brain Substantia Nigra	brain
23	chr12:50159000-50170200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:50159000-50170400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:50159000-50170400	Weak transcription	NH-A	brain
26	chr12:50159000-50170400	Weak transcription	Osteobl	bone
27	chr12:50159000-50171800	Weak transcription	Brain Anterior Caudate	brain
28	chr12:50159200-50161800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr12:50159200-50161800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr12:50159200-50162200	Weak transcription	Placenta	Placenta
31	chr12:50159200-50164200	Weak transcription	HSMM	muscle
32	chr12:50159200-50164400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr12:50159200-50170000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:50159200-50170000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:50159200-50170200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:50159200-50170200	Weak transcription	NHEK	skin
37	chr12:50159200-50170400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:50159200-50170400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:50159200-50170400	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr12:50159200-50170600	Weak transcription	HMEC	breast
41	chr12:50159200-50172200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr12:50159200-50177600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr12:50159400-50161800	Weak transcription	Fetal Brain Female	brain
44	chr12:50159400-50161800	Weak transcription	Left Ventricle	heart
45	chr12:50159400-50163600	Weak transcription	Fetal Intestine Large	intestine
46	chr12:50159400-50171800	Weak transcription	Liver	Liver
47	chr12:50159400-50178600	Weak transcription	Right Ventricle	heart
48	chr12:50159600-50162000	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr12:50159600-50163200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr12:50159800-50161800	Enhancers	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links