Variant report

Variant	rs1196848
Chromosome Location	chr12:105494962-105494963
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105493554..105497318-chr12:105498704..105503069,6	K562	blood:
2	chr12:105484191..105488176-chr12:105493160..105495554,3	MCF-7	breast:
3	chr12:105476974..105478534-chr12:105493271..105495502,2	K562	blood:
4	chr12:105481985..105484385-chr12:105492021..105495022,3	K562	blood:
5	chr12:105493621..105499511-chr12:105499874..105503218,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136010	Chromatin interaction
ENSG00000257999	Chromatin interaction
ENSG00000136051	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10746010	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778367	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[MKK][hapmap];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]
rs10861347	1.00[CHB][hapmap]
rs10861371	1.00[CHB][hapmap]
rs1107755	0.83[EUR][1000 genomes]
rs1107757	0.83[EUR][1000 genomes]
rs11112424	0.83[EUR][1000 genomes]
rs11112434	0.85[CEU][hapmap];1.00[CHB][hapmap];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	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196756	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196759	1.00[ASN][1000 genomes]
rs1196760	1.00[CHB][hapmap];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	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs1196780	0.85[CEU][hapmap];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	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs1196795	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs1196797	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs1196798	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];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	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196818	1.00[CHB][hapmap]
rs1196819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.83[MKK][hapmap];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[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196841	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196844	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]
rs1196851	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196852	1.00[CHB][hapmap]
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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196869	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196871	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196872	0.92[CEU][hapmap];1.00[GIH][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196873	1.00[CEU][hapmap];1.00[GIH][hapmap];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	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196884	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];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	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209637	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs1211276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211277	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]
rs12822081	1.00[CHB][hapmap]
rs1345096	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1444610	0.82[EUR][1000 genomes]
rs1621553	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1663564	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1663565	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1732370	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	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2374449	1.00[CEU][hapmap];0.85[GIH][hapmap];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	0.83[CEU][hapmap];1.00[CHB][hapmap];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	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2464181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464182	0.92[AFR][1000 genomes];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	1.00[CEU][hapmap];1.00[CHB][hapmap];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	1.00[CEU][hapmap];0.85[GIH][hapmap];0.88[EUR][1000 genomes]
rs6539183	1.00[CEU][hapmap];0.88[MKK][hapmap];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	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132624	0.90[EUR][1000 genomes]
rs7132855	1.00[CEU][hapmap];0.85[GIH][hapmap];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	1.00[CEU][hapmap];0.88[MKK][hapmap];0.84[EUR][1000 genomes]
rs873119	0.84[EUR][1000 genomes]
rs935240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];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	0.85[CEU][hapmap];1.00[CHB][hapmap];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: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
rs1196848	ALDH1L2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105494000-105495000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr12:105494000-105495000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:105494000-105495000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr12:105494200-105495000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr12:105494200-105495000	Enhancers	NHDF-Ad	bronchial
6	chr12:105494200-105495200	Enhancers	HSMM	muscle
7	chr12:105494400-105495000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
8	chr12:105494600-105495000	Enhancers	Hela-S3	cervix
9	chr12:105494600-105495000	Enhancers	Osteobl	bone
10	chr12:105494600-105500200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:105494800-105495200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:105494800-105495200	Enhancers	A549	lung
13	chr12:105494800-105495200	Enhancers	HepG2	liver
14	chr12:105494800-105495200	Weak transcription	NHLF	lung
15	chr12:105494800-105500000	Weak transcription	NHEK	skin
16	chr12:105494800-105500200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:105494800-105500200	Weak transcription	HMEC	breast
18	chr12:105494800-105500600	Weak transcription	NH-A	brain

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