Variant report

Variant	rs2166142
Chromosome Location	chr12:105479698-105479699
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:105479649-105479699	AG04449	skin:	fetal
2	chr12:105479649-105479699	BE2_C	brain:	n/a
3	chr12:105479649-105479699	IMR90	lung:	fetal
4	chr12:105479649-105479699	GM12878	blood:	n/a
5	chr12:105479649-105479699	Jurkat	blood:	n/a
6	chr12:105479649-105479699	NT2-D1	testis:	n/a
7	chr12:105479649-105479699	NHBE	bronchial:	n/a
8	chr12:105479649-105479699	RPTEC	kidney:	n/a
9	chr12:105479649-105479699	SK-N-MC	brain:	n/a
10	chr12:105479649-105479699	AG09319	gingival:	n/a
11	chr12:105479649-105479699	MCF10A-Er-Src	breast:	n/a
12	chr12:105479649-105479699	A549	lung:	n/a
13	chr12:105479649-105479699	NB4	blood:	n/a
14	chr12:105479649-105479699	HMEC	breast:	n/a
15	chr12:105479649-105479699	NH-A	brain:	n/a
16	chr12:105479649-105479699	HepG2	liver:	n/a
17	chr12:105479649-105479699	U87	brain:	n/a
18	chr12:105479649-105479699	SK-N-SH	brain:	n/a
19	chr12:105479649-105479699	HIPEpiC	eye:	n/a
20	chr12:105479649-105479699	PFSK-1	brain:	n/a
21	chr12:105479649-105479699	ECC-1	luminal epithelium:	n/a
22	chr12:105479649-105479699	K562	blood:	n/a
23	chr12:105479649-105479699	Hepatocyte	liver:	n/a
24	chr12:105479649-105479699	HPAEpiC	pulmonary alveolar:	n/a
25	chr12:105479649-105479699	HCT-116	colon:	n/a
26	chr12:105479649-105479699	HRPEpiC	eye:	n/a
27	chr12:105479649-105479699	PANC-1	pancreas:	n/a
28	chr12:105479649-105479699	SKMC	muscle:	n/a
29	chr12:105479649-105479699	HRCEpiC	kidney:	n/a
30	chr12:105479649-105479699	HRE	kidney:	n/a
31	chr12:105479649-105479699	LNCaP	prostate:	n/a
32	chr12:105479649-105479699	ProgFib	skin:	n/a
33	chr12:105479649-105479699	GM12892	blood:	n/a
34	chr12:105479649-105479699	AG09309	skin:	n/a
35	chr12:105479649-105479699	SAEC	small airway:	n/a
36	chr12:105479649-105479699	NHDF-neo	bronchial:	n/a
37	chr12:105479649-105479699	HAEpiC	amniotic membrane:	n/a
38	chr12:105479649-105479699	HCF	heart:	n/a
39	chr12:105479649-105479699	GM19239	blood:	n/a
40	chr12:105479649-105479699	AG04450	lung:	fetal
41	chr12:105479649-105479699	SK-N-SH_RA	brain:	n/a
42	chr12:105479649-105479699	PrEC	prostate:	n/a
43	chr12:105479649-105479699	HCPEpiC	choroid plexus:	n/a
44	chr12:105479649-105479699	GM12891	blood:	n/a
45	chr12:105479649-105479699	HUVEC	blood vessel:	n/a
46	chr12:105479649-105479699	AoSMC	blood vessel:	n/a
47	chr12:105479649-105479699	HEEpiC	esophagus:	n/a
48	chr12:105479649-105479699	HNPCEpiC	eye:	n/a
49	chr12:105479649-105479699	HCM	heart:	n/a
50	chr12:105479649-105479699	BJ	skin:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105477772..105479851-chr12:105501425..105505225,4	MCF-7	breast:
2	chr12:105477899..105479847-chr12:105501301..105502988,2	MCF-7	breast:

No data

Variant related genes	Relation type
ALDH1L2	CpG island
ENSG00000136051	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10746010	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778367	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778368	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778369	0.92[EUR][1000 genomes]
rs1196742	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196745	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196748	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196749	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196753	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196754	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196756	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196759	1.00[ASN][1000 genomes]
rs1196760	1.00[ASN][1000 genomes]
rs1196764	0.89[EUR][1000 genomes]
rs1196765	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196770	0.82[EUR][1000 genomes]
rs1196772	0.82[EUR][1000 genomes]
rs1196777	0.81[EUR][1000 genomes]
rs1196798	0.89[EUR][1000 genomes]
rs1196800	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196801	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196805	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196806	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196807	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196808	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196811	0.89[EUR][1000 genomes]
rs1196813	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196817	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196819	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196820	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196823	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196825	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196831	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196833	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196839	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196841	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196842	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196844	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196848	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196851	0.88[EUR][1000 genomes]
rs1196853	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196857	1.00[ASN][1000 genomes]
rs1196859	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196861	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196862	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196864	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196869	0.89[EUR][1000 genomes]
rs1196871	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196872	0.88[EUR][1000 genomes]
rs1196873	0.89[EUR][1000 genomes]
rs1196874	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196881	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196884	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196885	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1206559	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209308	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211276	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211277	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1345096	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1621553	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1663564	1.00[ASN][1000 genomes]
rs1663565	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1732370	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246243	0.82[EUR][1000 genomes]
rs2257156	0.88[EUR][1000 genomes]
rs2374449	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2440692	0.87[EUR][1000 genomes]
rs2440714	0.91[EUR][1000 genomes]
rs2440715	1.00[ASN][1000 genomes]
rs2440718	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464173	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464175	0.89[EUR][1000 genomes]
rs2464181	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464182	0.87[EUR][1000 genomes]
rs4356312	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4356313	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4372534	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4390426	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964122	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964331	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6539183	0.86[EUR][1000 genomes]
rs6539186	0.87[EUR][1000 genomes]
rs6539187	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539188	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7132040	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132624	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7132855	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71441895	0.82[EUR][1000 genomes]
rs7299701	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7302854	0.87[EUR][1000 genomes]
rs7303961	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7963877	0.86[EUR][1000 genomes]
rs935240	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935241	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935242	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935244	0.82[EUR][1000 genomes]
rs935246	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935248	0.89[EUR][1000 genomes]
rs935249	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	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
rs2166142	ALDH1L2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105478800-105480200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr12:105478800-105483200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:105478800-105483400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr12:105478800-105483600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr12:105478800-105483600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:105478800-105483800	Weak transcription	K562	blood
7	chr12:105478800-105486200	Weak transcription	Right Atrium	heart
8	chr12:105479200-105482800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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