Variant report

Variant	rs6441275
Chromosome Location	chr3:159501673-159501674
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	chr3:159481520..159484319-chr3:159499469..159501812,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250588	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11919032	1.00[CHD][hapmap]
rs13070254	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1461103	0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463514	0.96[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1675497	0.85[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes]
rs1965998	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2126143	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2169303	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2886623	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33050	1.00[JPT][hapmap]
rs33054	1.00[JPT][hapmap]
rs33056	1.00[JPT][hapmap]
rs3851360	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3863075	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3889311	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3911714	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4513503	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680520	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680527	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6441274	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788052	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6802934	0.83[AMR][1000 genomes]
rs6805556	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7625089	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7630289	1.00[CHD][hapmap]
rs7636819	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820045	0.86[AMR][1000 genomes];0.85[EUR][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	nsv4084	chr3:159492488-159513251	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6441275	IQCJ,SCHIP1	cis	intralobular white matter	BrainEAC
rs6441275	IQCJ,SCHIP1	cis	brain	BrainEAC
rs6441275	SCHIP1	cis	lymphoblastoid	seeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159484400-159505400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:159493600-159504400	Weak transcription	Right Atrium	heart
3	chr3:159493600-159505200	Weak transcription	Lung	lung
4	chr3:159493600-159505400	Weak transcription	Fetal Stomach	stomach
5	chr3:159493600-159509200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr3:159493600-159516200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:159493800-159502800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:159494800-159503000	Weak transcription	NHDF-Ad	bronchial
9	chr3:159495000-159502000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:159495000-159503000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:159495000-159503200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:159495200-159502000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr3:159495200-159502600	Weak transcription	HUVEC	blood vessel
14	chr3:159495200-159503000	Weak transcription	NHLF	lung
15	chr3:159495200-159503200	Weak transcription	Adipose Nuclei	Adipose
16	chr3:159495200-159504400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:159495200-159504600	Weak transcription	HSMMtube	muscle
18	chr3:159498600-159504400	Weak transcription	Esophagus	oesophagus
19	chr3:159499200-159502600	Enhancers	Stomach Smooth Muscle	stomach
20	chr3:159499400-159502400	Enhancers	Brain Angular Gyrus	brain
21	chr3:159499600-159501800	Weak transcription	Fetal Kidney	kidney
22	chr3:159499600-159501800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr3:159499800-159503400	Enhancers	Brain Cingulate Gyrus	brain
24	chr3:159499800-159506400	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr3:159500000-159503600	Enhancers	Brain Hippocampus Middle	brain
26	chr3:159500400-159509200	Enhancers	HepG2	liver
27	chr3:159500600-159501800	Enhancers	Left Ventricle	heart
28	chr3:159500600-159502000	Enhancers	Rectal Smooth Muscle	rectum
29	chr3:159500800-159501800	Weak transcription	Fetal Intestine Large	intestine
30	chr3:159500800-159501800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr3:159500800-159502800	Weak transcription	Stomach Mucosa	stomach
32	chr3:159501000-159501800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr3:159501000-159502200	Enhancers	A549	lung
34	chr3:159501000-159502800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:159501000-159503400	Enhancers	Placenta	Placenta
36	chr3:159501000-159508000	Enhancers	Colon Smooth Muscle	Colon
37	chr3:159501200-159502400	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr3:159501200-159502800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:159501200-159502800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:159501200-159503400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:159501200-159503400	Enhancers	Placenta Amnion	Placenta Amnion
42	chr3:159501200-159503400	Flanking Active TSS	NHEK	skin
43	chr3:159501200-159504400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:159501200-159506200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:159501400-159501800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:159501400-159501800	Weak transcription	Brain Substantia Nigra	brain
47	chr3:159501400-159502600	Weak transcription	Osteobl	bone
48	chr3:159501400-159502800	Flanking Active TSS	HMEC	breast
49	chr3:159501400-159503400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:159501400-159503400	Enhancers	Aorta	Aorta

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