Variant report

Variant	rs1196881
Chromosome Location	chr12:105485885-105485886
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105485255..105487201-chr12:105499969..105501573,2	K562	blood:
2	chr12:105484191..105488176-chr12:105493160..105495554,3	MCF-7	breast:
3	chr12:105351971..105353693-chr12:105484339..105486678,2	MCF-7	breast:
4	chr12:105467422..105469473-chr12:105483302..105486142,2	K562	blood:

Variant related genes	Relation type
ENSG00000257999	Chromatin interaction
ENSG00000136051	Chromatin interaction
ENSG00000136052	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10746010	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778367	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778368	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778369	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10861347	1.00[CHB][hapmap]
rs10861371	1.00[CHB][hapmap]
rs11112434	1.00[CHB][hapmap]
rs1196742	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196745	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196748	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196749	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196753	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196754	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196756	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[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	0.91[EUR][1000 genomes]
rs1196765	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196770	0.84[EUR][1000 genomes]
rs1196772	0.84[EUR][1000 genomes]
rs1196777	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs1196793	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs1196798	0.89[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1196800	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196801	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196805	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196806	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196807	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196808	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196811	0.92[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1196813	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196817	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196818	1.00[CHB][hapmap]
rs1196819	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196820	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196823	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196825	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196831	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196833	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196839	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196841	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196842	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196844	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196848	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]
rs1196851	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1196852	1.00[CHB][hapmap]
rs1196853	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196857	1.00[ASN][1000 genomes]
rs1196859	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196861	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196862	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196864	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196869	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1196871	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196872	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1196873	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1196874	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196884	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196885	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1206559	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209308	0.90[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1210669	0.81[EUR][1000 genomes]
rs1211276	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211277	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12822081	1.00[CHB][hapmap]
rs1345096	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1621553	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1663564	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1663565	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1732370	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166142	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246243	0.84[EUR][1000 genomes]
rs2257156	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs2374449	0.92[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2440692	0.89[EUR][1000 genomes]
rs2440714	0.93[EUR][1000 genomes]
rs2440715	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2440718	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464173	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464175	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2464181	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464182	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4356312	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4356313	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4372534	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4390426	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964122	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964331	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6539183	0.92[CEU][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6539186	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6539187	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539188	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7132040	0.92[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132624	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7132855	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71441895	0.84[EUR][1000 genomes]
rs7299701	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7302854	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7303961	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7963877	0.92[CEU][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs935240	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935241	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935242	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935244	1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs935246	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935248	0.91[EUR][1000 genomes]
rs935249	0.81[AMR][1000 genomes];0.90[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
rs1196881	ALDH1L2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105478800-105486200	Weak transcription	Right Atrium	heart
2	chr12:105483200-105487000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:105484400-105486600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:105484800-105487000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:105485200-105486000	Enhancers	H9 Cell Line	embryonic stem cell
6	chr12:105485200-105486000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr12:105485400-105486000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr12:105485400-105486000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr12:105485400-105486200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:105485400-105486400	Enhancers	K562	blood
11	chr12:105485400-105486800	Enhancers	Brain Substantia Nigra	brain
12	chr12:105485400-105486800	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr12:105485600-105486000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:105485600-105486000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr12:105485600-105486000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr12:105485600-105486000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr12:105485600-105486000	Flanking Active TSS	HMEC	breast
18	chr12:105485600-105486200	Active TSS	NHEK	skin
19	chr12:105485600-105486600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr12:105485800-105486200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:105485800-105486200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:105485800-105486200	Bivalent Enhancer	HepG2	liver
23	chr12:105485800-105486400	Active TSS	H1 Cell Line	embryonic stem cell
24	chr12:105485800-105486400	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr12:105485800-105486400	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr12:105485800-105486400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:105485800-105486400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:105485800-105487000	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr12:105485800-105487000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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