Variant report

Variant	rs447861
Chromosome Location	chr1:220929492-220929493
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	chr1:220926710..220928570-chr1:220929149..220931113,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117791	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12408093	1.00[MEX][hapmap]
rs2275575	0.88[YRI][hapmap]
rs337138	0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs337143	0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs337145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs337149	1.00[ASN][1000 genomes]
rs337151	1.00[ASN][1000 genomes]
rs371348	1.00[ASW][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs434167	1.00[ASN][1000 genomes]
rs434188	0.94[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs453079	1.00[MEX][hapmap];0.88[MKK][hapmap]
rs7524572	1.00[MEX][hapmap]
rs774148	0.87[YRI][hapmap];1.00[ASN][1000 genomes]
rs774149	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]

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	nsv523389	chr1:220926844-220956012	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs447861	RAI14	trans	lymphoblastoid	seeQTL
rs447861	APLP2	trans	lymphoblastoid	seeQTL
rs447861	T	trans	lymphoblastoid	seeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220922400-220932200	Weak transcription	HSMMtube	muscle
2	chr1:220922600-220931000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:220922600-220943800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:220922600-220946400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:220922800-220959600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:220922800-220959600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:220923200-220930400	Weak transcription	Spleen	Spleen
8	chr1:220923200-220948000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:220924200-220931000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:220924200-220936000	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:220924600-220936800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:220924600-220944000	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:220924800-220931200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:220924800-220945600	Weak transcription	Osteobl	bone
15	chr1:220925000-220946000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:220925000-220959400	Weak transcription	Brain Angular Gyrus	brain
17	chr1:220925200-220942000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:220925200-220943400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:220925400-220950200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:220925800-220931800	Strong transcription	Fetal Intestine Small	intestine
21	chr1:220925800-220938400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:220927000-220933000	Weak transcription	Right Ventricle	heart
23	chr1:220927200-220933200	Weak transcription	Small Intestine	intestine
24	chr1:220927400-220929800	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr1:220927400-220930400	Strong transcription	Stomach Smooth Muscle	stomach
26	chr1:220927600-220930800	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr1:220927600-220931200	Strong transcription	Duodenum Mucosa	Duodenum
28	chr1:220927600-220931200	Strong transcription	Fetal Muscle Leg	muscle
29	chr1:220927600-220931200	Strong transcription	Hela-S3	cervix
30	chr1:220927600-220934400	Weak transcription	Stomach Mucosa	stomach
31	chr1:220927800-220929600	Strong transcription	HepG2	liver
32	chr1:220927800-220930800	Strong transcription	Gastric	stomach
33	chr1:220927800-220931000	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:220927800-220931000	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:220927800-220931200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:220927800-220931200	Strong transcription	Fetal Intestine Large	intestine
37	chr1:220927800-220931200	Strong transcription	Pancreas	Pancrea
38	chr1:220927800-220931400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr1:220927800-220931600	Strong transcription	Lung	lung
40	chr1:220927800-220938600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:220928000-220930200	Strong transcription	Colonic Mucosa	Colon
42	chr1:220928000-220931000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:220928000-220931200	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:220928000-220931200	Strong transcription	Fetal Muscle Trunk	muscle
45	chr1:220928000-220931200	Strong transcription	Ovary	ovary
46	chr1:220928000-220931200	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr1:220928000-220933600	Strong transcription	Fetal Stomach	stomach
48	chr1:220928200-220929800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:220928200-220930000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:220928200-220930000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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