Variant report

Variant	rs7969800
Chromosome Location	chr12:105649500-105649501
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105632034..105634612-chr12:105649228..105651077,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10778371	0.97[ASN][1000 genomes]
rs1109432	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11112436	0.83[EUR][1000 genomes]
rs1196750	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1196766	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1196767	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1196768	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1196776	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1196778	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1196779	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1196781	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1196785	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1196788	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1196804	0.83[EUR][1000 genomes]
rs1196809	0.83[EUR][1000 genomes]
rs1196814	0.83[EUR][1000 genomes]
rs1196822	0.82[EUR][1000 genomes]
rs1196835	0.82[EUR][1000 genomes]
rs1196836	0.82[EUR][1000 genomes]
rs1196854	0.84[EUR][1000 genomes]
rs1196856	0.85[EUR][1000 genomes]
rs1196860	0.82[EUR][1000 genomes]
rs1196866	0.85[EUR][1000 genomes]
rs1196867	0.83[EUR][1000 genomes]
rs1196868	0.85[EUR][1000 genomes]
rs1196878	0.82[EUR][1000 genomes]
rs1201657	0.85[EUR][1000 genomes]
rs1732378	0.85[EUR][1000 genomes]
rs1732379	0.85[EUR][1000 genomes]
rs2264066	0.84[EUR][1000 genomes]
rs2374448	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2440708	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2440717	0.83[EUR][1000 genomes]
rs4964127	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4964344	0.89[ASN][1000 genomes]
rs4964345	0.89[ASN][1000 genomes]
rs4964346	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6539196	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6539197	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs727888	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7300300	0.89[ASN][1000 genomes]
rs7309320	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7310488	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7974354	0.84[ASN][1000 genomes]
rs7974694	0.84[ASN][1000 genomes]
rs7978648	0.87[ASN][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	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
2	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
3	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
rs7969800	ALDH1L2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105646400-105651000	Enhancers	Osteobl	bone
2	chr12:105647000-105649600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:105647000-105650000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr12:105647000-105652600	Enhancers	HSMMtube	muscle
5	chr12:105647000-105653400	Enhancers	NHLF	lung
6	chr12:105647200-105651000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:105647200-105651800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:105647400-105653400	Enhancers	Placenta Amnion	Placenta Amnion
9	chr12:105647800-105649800	Weak transcription	Aorta	Aorta
10	chr12:105648000-105649600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr12:105648200-105649600	Weak transcription	K562	blood
12	chr12:105648200-105649800	Enhancers	NH-A	brain
13	chr12:105648200-105651000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:105648200-105651000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr12:105648200-105651800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:105648200-105651800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:105648200-105652000	Enhancers	HMEC	breast
18	chr12:105648200-105653000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:105648200-105653800	Enhancers	NHDF-Ad	bronchial
20	chr12:105648200-105657400	Weak transcription	Esophagus	oesophagus
21	chr12:105648400-105650400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr12:105648600-105650200	Enhancers	Muscle Satellite Cultured Cells	--
23	chr12:105648600-105650400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:105648800-105650000	Weak transcription	Hela-S3	cervix
25	chr12:105648800-105651800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:105648800-105651800	Enhancers	NHEK	skin
27	chr12:105648800-105652800	Enhancers	HSMM	muscle
28	chr12:105649000-105649600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:105649000-105649600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:105649000-105650800	Weak transcription	A549	lung
31	chr12:105649000-105651000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:105649200-105650400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:105649400-105649800	Weak transcription	HUVEC	blood vessel
34	chr12:105649400-105650000	Enhancers	Primary T cells from cord blood	blood

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