Variant report

Variant	rs1196841
Chromosome Location	chr12:105500631-105500632
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:105499892-105502605	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr12:105500463-105501689	MCF10A-Er-Src	breast:	n/a	chr12:105501493-105501504 chr12:105501493-105501504 chr12:105501492-105501500 chr12:105501494-105501503
3	MYC	chr12:105500615-105502478	K562	blood:	n/a	chr12:105502183-105502190 chr12:105501493-105501504 chr12:105502182-105502191 chr12:105501493-105501504 chr12:105501492-105501500 chr12:105501494-105501503
4	MXI1	chr12:105500112-105503958	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr12:105500593-105502415	GM12891	blood:	n/a	n/a
6	MYC	chr12:105500481-105502549	K562	blood:	n/a	chr12:105502183-105502190 chr12:105501493-105501504 chr12:105502182-105502191 chr12:105501493-105501504 chr12:105501492-105501500 chr12:105501494-105501503
7	HCFC1	chr12:105500332-105502938	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr12:105500589-105502152	K562	blood:	n/a	n/a
9	IRF1	chr12:105500557-105502264	K562	blood:	n/a	chr12:105502054-105502071 chr12:105502054-105502068 chr12:105501471-105501485 chr12:105502056-105502069 chr12:105502058-105502072 chr12:105502057-105502070 chr12:105502057-105502068 chr12:105502057-105502071 chr12:105502050-105502070 chr12:105502057-105502070 chr12:105502056-105502076 chr12:105502051-105502065 chr12:105502057-105502070 chr12:105502057-105502070
10	FOS	chr12:105500587-105501011	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr12:105500519-105502049	HepG2	liver:	n/a	n/a
12	MYC	chr12:105500414-105500787	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:105500524..105503114-chr12:106640734..106642263,2	MCF-7	breast:
2	chr12:105476762..105478986-chr12:105499431..105503042,4	K562	blood:
3	chr12:105379932..105381513-chr12:105500073..105501775,2	MCF-7	breast:
4	chr12:104530239..104532383-chr12:105499797..105502736,2	MCF-7	breast:
5	chr12:104681104..104682731-chr12:105500276..105502937,2	K562	blood:
6	chr12:105499144..105502991-chr12:105627617..105631044,5	MCF-7	breast:
7	chr12:105500023..105502355-chr12:105628064..105629909,2	K562	blood:
8	chr12:105478183..105481313-chr12:105498999..105500811,3	K562	blood:
9	chr12:104678772..104682731-chr12:105498551..105503490,6	K562	blood:
10	chr12:105500023..105504653-chr12:105628064..105630551,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ALDH1L2-1	chr12:105500566-105500957	ENSG00000257999.1

Variant related genes	Relation type
KIAA1033	TF binding region
ENSG00000136044	Chromatin interaction
ENSG00000136026	Chromatin interaction
ENSG00000151131	Chromatin interaction
ENSG00000235162	Chromatin interaction
ENSG00000120837	Chromatin interaction
ENSG00000198431	Chromatin interaction
ENSG00000258355	Chromatin interaction
ENSG00000136010	Chromatin interaction

Extended variants
information (count: 124 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10746010	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778367	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778368	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778369	0.86[EUR][1000 genomes]
rs1107755	0.83[EUR][1000 genomes]
rs1107757	0.83[EUR][1000 genomes]
rs11112424	0.83[EUR][1000 genomes]
rs11112434	0.83[EUR][1000 genomes]
rs1196742	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196745	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196748	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196749	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196753	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196754	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196756	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196759	1.00[ASN][1000 genomes]
rs1196760	1.00[ASN][1000 genomes]
rs1196764	0.99[EUR][1000 genomes]
rs1196765	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196770	0.92[EUR][1000 genomes]
rs1196772	0.92[EUR][1000 genomes]
rs1196777	0.91[EUR][1000 genomes]
rs1196780	0.84[EUR][1000 genomes]
rs1196782	0.83[EUR][1000 genomes]
rs1196786	0.83[EUR][1000 genomes]
rs1196787	0.82[EUR][1000 genomes]
rs1196789	0.82[EUR][1000 genomes]
rs1196793	0.83[EUR][1000 genomes]
rs1196795	0.81[EUR][1000 genomes]
rs1196797	0.83[EUR][1000 genomes]
rs1196798	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196800	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196801	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196805	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196806	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196807	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196808	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196811	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196813	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196817	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196819	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196820	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196823	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196825	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196831	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196833	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196834	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1196839	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196847	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1196848	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196851	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196853	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196857	1.00[ASN][1000 genomes]
rs1196859	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196861	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196862	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196864	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196869	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196871	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196872	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196873	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196874	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196881	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196884	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196885	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1206559	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209308	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209637	0.82[EUR][1000 genomes]
rs1211276	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211277	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211626	0.83[EUR][1000 genomes]
rs12369709	0.82[EUR][1000 genomes]
rs12814458	0.83[EUR][1000 genomes]
rs12816560	0.84[EUR][1000 genomes]
rs1345096	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1444610	0.82[EUR][1000 genomes]
rs1621553	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1663564	1.00[ASN][1000 genomes]
rs1663565	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1732370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166142	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246243	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2257156	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2374449	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2440692	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2440714	0.95[EUR][1000 genomes]
rs2440715	1.00[ASN][1000 genomes]
rs2440718	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464173	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464175	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2464181	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464182	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35679386	0.84[EUR][1000 genomes]
rs4356312	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4356313	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4372534	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4390426	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964122	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964331	0.88[EUR][1000 genomes]
rs6539183	0.84[EUR][1000 genomes]
rs6539186	0.85[EUR][1000 genomes]
rs6539187	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539188	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7132040	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132624	0.90[EUR][1000 genomes]
rs7132855	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71441895	0.92[EUR][1000 genomes]
rs7299701	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7302854	0.85[EUR][1000 genomes]
rs7303961	0.92[EUR][1000 genomes]
rs73181823	0.84[EUR][1000 genomes]
rs7963877	0.84[EUR][1000 genomes]
rs873119	0.84[EUR][1000 genomes]
rs935240	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935241	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935242	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935244	0.92[EUR][1000 genomes]
rs935246	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935248	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs935249	0.93[AMR][1000 genomes];0.98[EUR][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	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1196841	ALDH1L2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105495000-105500800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr12:105500200-105500800	Enhancers	Fetal Intestine Small	intestine
3	chr12:105500200-105501000	Flanking Active TSS	NHEK	skin
4	chr12:105500200-105501400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:105500200-105502400	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr12:105500200-105502400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:105500200-105502800	Active TSS	Cortex derived primary cultured neurospheres	brain
8	chr12:105500200-105503000	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr12:105500200-105504000	Active TSS	Brain Anterior Caudate	brain
10	chr12:105500400-105500800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:105500400-105500800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:105500400-105500800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
13	chr12:105500400-105500800	Flanking Active TSS	Liver	Liver
14	chr12:105500400-105500800	Flanking Active TSS	A549	lung
15	chr12:105500400-105500800	Enhancers	Hela-S3	cervix
16	chr12:105500400-105501000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:105500400-105501000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr12:105500400-105501000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:105500400-105501000	Flanking Active TSS	HMEC	breast
20	chr12:105500400-105502600	Active TSS	Fetal Brain Female	brain
21	chr12:105500400-105503200	Active TSS	Brain Angular Gyrus	brain
22	chr12:105500400-105503400	Active TSS	Stomach Smooth Muscle	stomach
23	chr12:105500400-105503800	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr12:105500400-105504600	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr12:105500400-105505000	Active TSS	K562	blood
26	chr12:105500600-105500800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:105500600-105500800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:105500600-105500800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
29	chr12:105500600-105500800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:105500600-105500800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr12:105500600-105500800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
32	chr12:105500600-105500800	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
33	chr12:105500600-105500800	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr12:105500600-105500800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:105500600-105500800	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 1	blood
36	chr12:105500600-105500800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr12:105500600-105500800	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr12:105500600-105500800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:105500600-105500800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr12:105500600-105500800	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr12:105500600-105500800	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr12:105500600-105500800	Flanking Active TSS	Fetal Brain Male	brain
43	chr12:105500600-105500800	Flanking Active TSS	Fetal Intestine Large	intestine
44	chr12:105500600-105500800	Flanking Active TSS	Fetal Lung	lung
45	chr12:105500600-105500800	Flanking Active TSS	Rectal Smooth Muscle	rectum
46	chr12:105500600-105500800	Active TSS	GM12878-XiMat	blood
47	chr12:105500600-105500800	Flanking Active TSS	NH-A	brain
48	chr12:105500600-105500800	Enhancers	NHDF-Ad	bronchial
49	chr12:105500600-105500800	Enhancers	NHLF	lung
50	chr12:105500600-105500800	Flanking Active TSS	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links