Variant report

Variant	rs873119
Chromosome Location	chr12:105628340-105628341
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:105628276-105630777	MCF10A-Er-Src	breast:	n/a	n/a
2	CTCF	chr12:105628280-105628430	GM12873	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:105606795..105619301-chr12:105624368..105633184,26	MCF-7	breast:
2	chr12:105599435..105602379-chr12:105626303..105628956,2	K562	blood:
3	chr12:105620755..105625323-chr12:105625745..105629848,5	K562	blood:
4	chr12:105609511..105612358-chr12:105625566..105629291,3	K562	blood:
5	chr12:105499144..105502991-chr12:105627617..105631044,5	MCF-7	breast:
6	chr12:105501540..105503183-chr12:105627693..105630661,2	MCF-7	breast:
7	chr12:105500023..105502355-chr12:105628064..105629909,2	K562	blood:
8	chr12:105500023..105504653-chr12:105628064..105630551,4	K562	blood:

No data

Variant related genes	Relation type
C12orf75	TF binding region
APPL2	TF binding region
ENSG00000136051	Chromatin interaction
ENSG00000257999	Chromatin interaction
ENSG00000136044	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1107755	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1107757	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11112424	0.96[EUR][1000 genomes]
rs11112428	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112434	0.94[EUR][1000 genomes]
rs1196742	0.85[EUR][1000 genomes]
rs1196744	0.84[ASN][1000 genomes]
rs1196745	0.85[EUR][1000 genomes]
rs1196748	0.85[EUR][1000 genomes]
rs1196749	0.85[EUR][1000 genomes]
rs1196753	0.89[EUR][1000 genomes]
rs1196754	0.89[EUR][1000 genomes]
rs1196756	0.85[EUR][1000 genomes]
rs1196764	0.85[EUR][1000 genomes]
rs1196765	0.85[EUR][1000 genomes]
rs1196770	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1196772	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1196777	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1196780	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196782	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1196786	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1196787	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196789	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196790	0.90[EUR][1000 genomes]
rs1196791	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1196793	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1196795	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1196797	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1196798	0.85[EUR][1000 genomes]
rs1196800	0.84[EUR][1000 genomes]
rs1196801	0.84[EUR][1000 genomes]
rs1196805	0.84[EUR][1000 genomes]
rs1196806	0.84[EUR][1000 genomes]
rs1196807	0.84[EUR][1000 genomes]
rs1196808	0.83[EUR][1000 genomes]
rs1196811	0.85[EUR][1000 genomes]
rs1196813	0.84[EUR][1000 genomes]
rs1196817	0.84[EUR][1000 genomes]
rs1196819	0.84[EUR][1000 genomes]
rs1196820	0.84[EUR][1000 genomes]
rs1196823	0.83[EUR][1000 genomes]
rs1196825	0.84[EUR][1000 genomes]
rs1196831	0.84[EUR][1000 genomes]
rs1196833	0.84[EUR][1000 genomes]
rs1196839	0.84[EUR][1000 genomes]
rs1196841	0.84[EUR][1000 genomes]
rs1196842	0.84[EUR][1000 genomes]
rs1196844	0.84[EUR][1000 genomes]
rs1196848	0.84[EUR][1000 genomes]
rs1196851	0.86[EUR][1000 genomes]
rs1196853	0.85[EUR][1000 genomes]
rs1196859	0.82[EUR][1000 genomes]
rs1196861	0.85[EUR][1000 genomes]
rs1196862	0.84[EUR][1000 genomes]
rs1196864	0.85[EUR][1000 genomes]
rs1196869	0.85[EUR][1000 genomes]
rs1196871	0.81[EUR][1000 genomes]
rs1196872	0.86[EUR][1000 genomes]
rs1196873	0.85[EUR][1000 genomes]
rs1196874	0.84[EUR][1000 genomes]
rs1206559	0.84[EUR][1000 genomes]
rs1209637	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211276	0.84[EUR][1000 genomes]
rs1211277	0.84[EUR][1000 genomes]
rs1211626	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12369709	0.94[EUR][1000 genomes]
rs12814458	0.96[EUR][1000 genomes]
rs12816560	0.95[EUR][1000 genomes]
rs1444610	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1663565	0.82[EUR][1000 genomes]
rs1732370	0.84[EUR][1000 genomes]
rs2257156	0.86[EUR][1000 genomes]
rs2440718	0.84[EUR][1000 genomes]
rs2464173	0.84[EUR][1000 genomes]
rs2464175	0.85[EUR][1000 genomes]
rs2464181	0.84[EUR][1000 genomes]
rs2464182	0.83[EUR][1000 genomes]
rs35679386	0.95[EUR][1000 genomes]
rs67604711	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71441895	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73181823	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs935240	0.84[EUR][1000 genomes]
rs935241	0.84[EUR][1000 genomes]
rs935242	0.84[EUR][1000 genomes]
rs935244	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs935248	0.85[EUR][1000 genomes]
rs935249	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv455704	chr12:105583877-105651356	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
3	nsv560053	chr12:105583877-105651356	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
4	nsv899499	chr12:105616297-105722529	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs873119	ALDH1L2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105605600-105628400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:105609200-105628600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr12:105616600-105629000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:105617000-105629000	Weak transcription	Esophagus	oesophagus
5	chr12:105617400-105629000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:105621800-105628600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr12:105621800-105628600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:105622000-105629000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:105622400-105628400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr12:105622800-105628400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:105623000-105628600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr12:105623400-105628600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr12:105623600-105628800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr12:105625000-105628800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:105625000-105628800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:105625600-105628600	Weak transcription	Placenta	Placenta
17	chr12:105625600-105629000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:105625600-105629000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:105625800-105628600	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr12:105625800-105628600	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr12:105626200-105628800	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr12:105626400-105628800	Enhancers	Primary B cells from cord blood	blood
23	chr12:105626400-105629400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:105626600-105628400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:105626600-105628800	Enhancers	Primary B cells from peripheral blood	blood
26	chr12:105626600-105628800	Flanking Active TSS	Brain Hippocampus Middle	brain
27	chr12:105626600-105629000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:105626600-105629200	Flanking Active TSS	Fetal Brain Female	brain
29	chr12:105626800-105628400	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr12:105626800-105628400	Flanking Active TSS	Brain Cingulate Gyrus	brain
31	chr12:105626800-105628600	Flanking Active TSS	Brain Angular Gyrus	brain
32	chr12:105626800-105628800	Enhancers	Stomach Mucosa	stomach
33	chr12:105626800-105629000	Flanking Active TSS	Brain Anterior Caudate	brain
34	chr12:105626800-105629000	Enhancers	Small Intestine	intestine
35	chr12:105627000-105628400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr12:105627000-105628400	Enhancers	HepG2	liver
37	chr12:105627000-105628800	Enhancers	Primary T cells fromperipheralblood	blood
38	chr12:105627000-105628800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr12:105627000-105628800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr12:105627000-105629000	Weak transcription	Lung	lung
41	chr12:105627000-105629400	Flanking Active TSS	Primary T cells from cord blood	blood
42	chr12:105627200-105628600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr12:105627200-105628600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr12:105627200-105628600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr12:105627200-105629000	Weak transcription	Gastric	stomach
46	chr12:105627200-105629000	Weak transcription	Pancreas	Pancrea
47	chr12:105627400-105628400	Flanking Active TSS	NHDF-Ad	bronchial
48	chr12:105627400-105628800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr12:105627400-105628800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr12:105627600-105628400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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