Variant report

Variant	rs12743529
Chromosome Location	chr1:84945434-84945435
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:84943777..84946552-chr1:84970497..84973179,2	MCF-7	breast:
2	chr1:84765283..84767308-chr1:84944913..84946542,2	K562	blood:
3	chr1:84943714..84946459-chr1:85038706..85040687,2	K562	blood:
4	chr1:84943703..84948095-chr1:85037647..85043843,8	K562	blood:
5	chr1:84765808..84767323-chr1:84944913..84947326,2	K562	blood:
6	chr1:84944684..84947410-chr1:84970225..84973395,6	MCF-7	breast:
7	chr1:84940376..84943283-chr1:84945216..84947221,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203943	Chromatin interaction
ENSG00000174021	Chromatin interaction
ENSG00000117151	Chromatin interaction
ENSG00000122432	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12031171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12408872	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830437	chr1:84837524-85001269	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12743529	RPF1	cis	parietal	SCAN
rs12743529	BCL10	cis	cerebellum	SCAN
rs12743529	SPATA1	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84944000-84945800	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr1:84944200-84945800	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr1:84944200-84946000	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr1:84944200-84946200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:84944200-84946200	Active TSS	Muscle Satellite Cultured Cells	--
6	chr1:84944200-84946200	Active TSS	A549	lung
7	chr1:84944200-84946400	Active TSS	Stomach Smooth Muscle	stomach
8	chr1:84944400-84945800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:84944400-84945800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:84944400-84945800	Active TSS	Liver	Liver
11	chr1:84944400-84945800	Active TSS	Brain Substantia Nigra	brain
12	chr1:84944400-84945800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
13	chr1:84944400-84945800	Active TSS	Fetal Brain Male	brain
14	chr1:84944400-84945800	Active TSS	Left Ventricle	heart
15	chr1:84944400-84945800	Active TSS	Rectal Mucosa Donor 31	rectum
16	chr1:84944400-84945800	Active TSS	NH-A	brain
17	chr1:84944400-84945800	Active TSS	Osteobl	bone
18	chr1:84944400-84946000	Active TSS	H9 Cell Line	embryonic stem cell
19	chr1:84944400-84946000	Active TSS	Ovary	ovary
20	chr1:84944400-84946000	Active TSS	Stomach Mucosa	stomach
21	chr1:84944400-84946200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:84944400-84946200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:84944400-84946200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:84944400-84946200	Active TSS	Colonic Mucosa	Colon
25	chr1:84944400-84946200	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr1:84944400-84946200	Active TSS	Hela-S3	cervix
27	chr1:84944400-84946200	Active TSS	HSMM	muscle
28	chr1:84944400-84946200	Active TSS	HSMMtube	muscle
29	chr1:84944400-84946400	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr1:84944400-84946400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:84944400-84946400	Active TSS	NHLF	lung
32	chr1:84944400-84946600	Active TSS	Psoas Muscle	Psoas
33	chr1:84944400-84946600	Active TSS	NHDF-Ad	bronchial
34	chr1:84944400-84947000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:84944600-84945600	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr1:84944600-84945600	Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr1:84944600-84945600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:84944600-84945600	Active TSS	Thymus	Thymus
39	chr1:84944600-84945800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:84944600-84945800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:84944600-84945800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:84944600-84945800	Active TSS	Brain Cingulate Gyrus	brain
43	chr1:84944600-84945800	Active TSS	Colon Smooth Muscle	Colon
44	chr1:84944600-84945800	Active TSS	Fetal Brain Female	brain
45	chr1:84944600-84945800	Active TSS	Pancreas	Pancrea
46	chr1:84944600-84946000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr1:84944600-84946000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:84944600-84946000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:84944600-84946000	Active TSS	Esophagus	oesophagus
50	chr1:84944600-84946000	Active TSS	Fetal Kidney	kidney

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