Variant report

Variant	rs1411479
Chromosome Location	chr1:181006930-181006931
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:181006288..181011234-chr1:181054894..181059610,7	MCF-7	breast:
2	chr1:180990408..180995619-chr1:181003343..181007035,5	K562	blood:
3	chr1:181006298..181009433-chr1:181068869..181071626,3	MCF-7	breast:
4	chr1:180997971..181011022-chr1:181054648..181063248,33	K562	blood:
5	chr1:181006277..181007828-chr1:181072524..181074862,2	MCF-7	breast:
6	chr1:180990645..180992975-chr1:181006730..181008328,2	MCF-7	breast:
7	chr1:181003253..181008679-chr1:181011469..181014538,5	MCF-7	breast:
8	chr1:180999745..181016101-chr1:181055432..181063450,33	K562	blood:
9	chr1:180987722..180989814-chr1:181005943..181007789,2	MCF-7	breast:
10	chr1:181006689..181009115-chr1:181111190..181112920,2	MCF-7	breast:
11	chr1:181004593..181007804-chr1:181008315..181013552,8	K562	blood:
12	chr1:181004788..181008643-chr1:181010792..181015908,7	K562	blood:
13	chr1:181005039..181007086-chr1:181081711..181083866,2	MCF-7	breast:
14	chr1:180993123..180994756-chr1:181005532..181007495,2	MCF-7	breast:
15	chr1:181004789..181007713-chr1:181048831..181050850,2	K562	blood:
16	chr1:181006912..181008596-chr1:181114437..181116744,2	MCF-7	breast:
17	chr1:181003285..181010147-chr1:181055895..181060690,15	MCF-7	breast:
18	chr1:180996013..180998343-chr1:181005290..181006932,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000135823	Chromatin interaction
ENSG00000272198	Chromatin interaction
ENSG00000162783	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10494536	0.92[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs10797662	0.85[EUR][1000 genomes]
rs10797663	0.84[EUR][1000 genomes]
rs10797665	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11584852	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12752307	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2225332	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3827708	0.92[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs6425659	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs6684455	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7546157	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs7556005	0.96[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap]
rs883859	0.91[CEU][hapmap];0.81[JPT][hapmap]

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	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	esv3342865	chr1:180933678-181018012	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv3383831	chr1:180937224-181029755	Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv1011081	chr1:180973159-181135953	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1411479	RGS8	cis	parietal	SCAN
rs1411479	SOAT1	cis	cerebellum	SCAN
rs1411479	STX6	cis	parietal	SCAN
rs1411479	PAPPA2	cis	cerebellum	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:181002600-181012200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:181003800-181009600	Weak transcription	Fetal Intestine Small	intestine
3	chr1:181003800-181012200	Weak transcription	Placenta	Placenta
4	chr1:181004000-181007000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:181004000-181008000	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr1:181004000-181008400	Weak transcription	Hela-S3	cervix
7	chr1:181004000-181008600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr1:181004000-181009400	Weak transcription	Stomach Mucosa	stomach
9	chr1:181004000-181009600	Weak transcription	A549	lung
10	chr1:181004000-181010000	Weak transcription	NHDF-Ad	bronchial
11	chr1:181004000-181010200	Weak transcription	Osteobl	bone
12	chr1:181004000-181010400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:181004000-181010400	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:181004000-181010600	Weak transcription	HMEC	breast
15	chr1:181004000-181012000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:181004000-181012000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:181004000-181013600	Weak transcription	Psoas Muscle	Psoas
18	chr1:181004000-181015600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:181004000-181025400	Weak transcription	Fetal Stomach	stomach
20	chr1:181004000-181025800	Weak transcription	Fetal Muscle Leg	muscle
21	chr1:181004000-181026200	Weak transcription	Brain Anterior Caudate	brain
22	chr1:181004200-181007800	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr1:181004200-181008200	Weak transcription	NHLF	lung
24	chr1:181004200-181010200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr1:181004200-181010600	Weak transcription	NHEK	skin
26	chr1:181004200-181012200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:181005000-181011800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:181005200-181011800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr1:181005200-181012200	Weak transcription	Lung	lung
30	chr1:181005400-181007000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr1:181005400-181009400	Weak transcription	Liver	Liver
32	chr1:181005400-181012000	Weak transcription	Adipose Nuclei	Adipose
33	chr1:181005400-181012200	Weak transcription	Colonic Mucosa	Colon
34	chr1:181005600-181007000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:181005600-181007000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:181005600-181007200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:181005600-181007600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr1:181005600-181009600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr1:181005600-181010400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:181005600-181010400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:181005600-181010400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr1:181005600-181012200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr1:181005600-181013800	Weak transcription	Pancreas	Pancrea
44	chr1:181005600-181025800	Weak transcription	Right Ventricle	heart
45	chr1:181005600-181026000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr1:181005600-181026400	Weak transcription	Colon Smooth Muscle	Colon
47	chr1:181005600-181028200	Weak transcription	Gastric	stomach
48	chr1:181005600-181028600	Weak transcription	Ovary	ovary
49	chr1:181005800-181007000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:181005800-181008000	Enhancers	Primary T helper naive cells from peripheral blood	blood

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