Variant report

Variant	rs13094970
Chromosome Location	chr3:156815280-156815281
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156813972..156815695-chr3:156823705..156826230,2	MCF-7	breast:
2	chr3:156814840..156817807-chr3:156824843..156827146,2	K562	blood:
3	chr3:156814290..156816114-chr3:156822905..156825348,2	K562	blood:
4	chr3:156813654..156815672-chr3:156844907..156847092,2	K562	blood:
5	chr3:156813189..156821079-chr3:156821537..156824673,9	K562	blood:
6	chr3:156806626..156809552-chr3:156813970..156817154,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241135	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs13072135	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13072757	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1384539	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1384540	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34122975	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35649103	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59634016	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349885	chr3:156685409-156878910	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
2	nsv829766	chr3:156811536-157020551	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13094970	RGS9	trans	cerebellum	SCAN
rs13094970	PLSCR2	trans	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156807600-156815800	Weak transcription	HSMMtube	muscle
2	chr3:156807800-156816200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:156807800-156822000	Weak transcription	Aorta	Aorta
4	chr3:156808600-156821600	Weak transcription	Small Intestine	intestine
5	chr3:156810400-156817600	Weak transcription	Lung	lung
6	chr3:156810600-156816200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:156810600-156832000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:156811000-156823000	Weak transcription	Spleen	Spleen
9	chr3:156811200-156817800	Weak transcription	Psoas Muscle	Psoas
10	chr3:156811400-156818600	Weak transcription	Fetal Intestine Large	intestine
11	chr3:156811600-156815600	Weak transcription	GM12878-XiMat	blood
12	chr3:156811800-156821000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr3:156812600-156815400	Enhancers	Left Ventricle	heart
14	chr3:156812800-156816200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:156812800-156816600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:156812800-156817000	Weak transcription	K562	blood
17	chr3:156812800-156818000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr3:156813000-156815600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:156813000-156815600	Weak transcription	NH-A	brain
20	chr3:156813000-156816200	Weak transcription	HMEC	breast
21	chr3:156813000-156818400	Weak transcription	Fetal Intestine Small	intestine
22	chr3:156813200-156815800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:156813200-156816000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:156813200-156816200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:156813200-156816200	Weak transcription	NHEK	skin
26	chr3:156813200-156816200	Weak transcription	NHLF	lung
27	chr3:156813200-156817200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:156813200-156838000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:156813400-156815400	Enhancers	Right Ventricle	heart
30	chr3:156813400-156816200	Weak transcription	Right Atrium	heart
31	chr3:156813400-156817800	Enhancers	Fetal Heart	heart
32	chr3:156813600-156815400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:156813600-156815400	Weak transcription	HSMM	muscle
34	chr3:156814400-156815400	Enhancers	Pancreas	Pancrea
35	chr3:156815000-156819800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:156815200-156821200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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