Variant report

Variant	rs1196786
Chromosome Location	chr12:105631160-105631161
allele	A/G
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:6)
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	chr12:105631137-105631290	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr12:105631107-105631319	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:105606795..105619301-chr12:105624368..105633184,26	MCF-7	breast:
2	chr12:105628750..105631438-chr12:105722608..105725285,3	MCF-7	breast:
3	chr12:105610784..105617210-chr12:105628529..105631630,8	MCF-7	breast:
4	chr12:105529161..105531125-chr12:105630136..105632646,2	K562	blood:
5	chr12:105630089..105632839-chr12:105665320..105668612,3	MCF-7	breast:
6	chr12:105542946..105545712-chr12:105628511..105631314,2	MCF-7	breast:

No data

Variant related genes	Relation type
APPL2	TF binding region
ENSG00000235162	Chromatin interaction
ENSG00000136051	Chromatin interaction
ENSG00000136044	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1107755	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1107757	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11112424	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11112428	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11112434	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1196742	0.84[EUR][1000 genomes]
rs1196745	0.84[EUR][1000 genomes]
rs1196748	0.84[EUR][1000 genomes]
rs1196749	0.84[EUR][1000 genomes]
rs1196753	0.88[EUR][1000 genomes]
rs1196754	0.88[EUR][1000 genomes]
rs1196756	0.84[EUR][1000 genomes]
rs1196764	0.83[EUR][1000 genomes]
rs1196765	0.84[EUR][1000 genomes]
rs1196770	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1196772	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1196777	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1196780	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1196782	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196787	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196789	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196790	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1196791	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1196793	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1196795	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1196797	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196798	0.84[EUR][1000 genomes]
rs1196800	0.83[EUR][1000 genomes]
rs1196801	0.83[EUR][1000 genomes]
rs1196805	0.83[EUR][1000 genomes]
rs1196806	0.83[EUR][1000 genomes]
rs1196807	0.83[EUR][1000 genomes]
rs1196808	0.82[EUR][1000 genomes]
rs1196811	0.84[EUR][1000 genomes]
rs1196813	0.83[EUR][1000 genomes]
rs1196817	0.83[EUR][1000 genomes]
rs1196819	0.83[EUR][1000 genomes]
rs1196820	0.83[EUR][1000 genomes]
rs1196823	0.82[EUR][1000 genomes]
rs1196825	0.83[EUR][1000 genomes]
rs1196831	0.83[EUR][1000 genomes]
rs1196833	0.83[EUR][1000 genomes]
rs1196839	0.83[EUR][1000 genomes]
rs1196841	0.83[EUR][1000 genomes]
rs1196842	0.83[EUR][1000 genomes]
rs1196844	0.83[EUR][1000 genomes]
rs1196848	0.83[EUR][1000 genomes]
rs1196851	0.83[EUR][1000 genomes]
rs1196853	0.84[EUR][1000 genomes]
rs1196859	0.81[EUR][1000 genomes]
rs1196861	0.84[EUR][1000 genomes]
rs1196862	0.83[EUR][1000 genomes]
rs1196864	0.84[EUR][1000 genomes]
rs1196869	0.82[EUR][1000 genomes]
rs1196872	0.83[EUR][1000 genomes]
rs1196873	0.82[EUR][1000 genomes]
rs1196874	0.83[EUR][1000 genomes]
rs1206559	0.83[EUR][1000 genomes]
rs1209637	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1211276	0.83[EUR][1000 genomes]
rs1211277	0.83[EUR][1000 genomes]
rs1211626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369709	0.97[EUR][1000 genomes]
rs12814458	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12816560	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1444610	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1663565	0.81[EUR][1000 genomes]
rs17036705	0.83[ASN][1000 genomes]
rs17036728	0.83[ASN][1000 genomes]
rs1732370	0.83[EUR][1000 genomes]
rs2257156	0.83[EUR][1000 genomes]
rs2272491	0.88[ASN][1000 genomes]
rs2289773	0.81[ASN][1000 genomes]
rs2293642	0.93[ASN][1000 genomes]
rs2440718	0.83[EUR][1000 genomes]
rs2464173	0.83[EUR][1000 genomes]
rs2464175	0.82[EUR][1000 genomes]
rs2464181	0.83[EUR][1000 genomes]
rs2464182	0.82[EUR][1000 genomes]
rs35679386	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3794234	0.93[ASN][1000 genomes]
rs3794235	0.93[ASN][1000 genomes]
rs61005937	0.95[ASN][1000 genomes]
rs67604711	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71441895	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73181823	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs873119	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs935240	0.83[EUR][1000 genomes]
rs935241	0.83[EUR][1000 genomes]
rs935242	0.83[EUR][1000 genomes]
rs935244	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs935248	0.84[EUR][1000 genomes]
rs935249	0.83[EUR][1000 genomes]
rs9788027	0.90[ASN][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
rs1196786	ALDH1L2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105630200-105633200	Weak transcription	Gastric	stomach
2	chr12:105630600-105631400	Enhancers	Thymus	Thymus
3	chr12:105630600-105633000	Weak transcription	Fetal Intestine Small	intestine
4	chr12:105630600-105633600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:105630600-105633800	Weak transcription	Primary T cells from cord blood	blood
6	chr12:105630600-105634000	Weak transcription	Primary B cells from cord blood	blood
7	chr12:105630800-105631400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:105630800-105631400	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr12:105630800-105631600	Enhancers	NHDF-Ad	bronchial
10	chr12:105630800-105632200	Weak transcription	Psoas Muscle	Psoas
11	chr12:105630800-105632200	Weak transcription	Stomach Mucosa	stomach
12	chr12:105630800-105632200	Weak transcription	HepG2	liver
13	chr12:105630800-105632800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr12:105630800-105632800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:105630800-105632800	Weak transcription	Osteobl	bone
16	chr12:105630800-105633000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:105630800-105633000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:105630800-105633000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr12:105630800-105633000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:105630800-105633000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr12:105630800-105633400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr12:105630800-105633400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr12:105630800-105633600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr12:105630800-105633600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr12:105630800-105633600	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr12:105630800-105633600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:105630800-105633800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr12:105630800-105633800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr12:105630800-105633800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr12:105630800-105633800	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr12:105630800-105634200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr12:105630800-105634200	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr12:105630800-105634400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr12:105630800-105639000	Weak transcription	Pancreas	Pancrea
35	chr12:105630800-105639000	Weak transcription	NHLF	lung

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