Variant report

Variant	rs1179441
Chromosome Location	chr12:120794653-120794654
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:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:120794109..120796035-chr12:120875633..120877623,4	MCF-7	breast:
2	chr12:120787191..120790083-chr12:120792780..120795331,2	MCF-7	breast:
3	chr12:120729032..120731045-chr12:120794243..120796110,2	K562	blood:
4	chr12:120793994..120794835-chr7:43878124..43878739,2	K562	blood:
5	chr12:120793772..120796303-chr12:120865942..120868774,2	MCF-7	breast:
6	chr12:120727859..120730082-chr12:120793938..120796016,2	MCF-7	breast:
7	chr12:120793939..120795057-chr12:120867907..120868976,15	K562	blood:
8	chr12:120793332..120795450-chr12:120874318..120875954,2	K562	blood:
9	chr12:120794442..120794968-chr12:120906277..120906800,2	K562	blood:
10	chr12:120793158..120796166-chr12:120882003..120884232,3	K562	blood:
11	chr12:120794499..120796527-chr12:120866923..120868493,2	K562	blood:
12	chr12:120794069..120794978-chr12:120804760..120805597,2	MCF-7	breast:
13	chr12:120666353..120667903-chr12:120793999..120796397,2	MCF-7	breast:
14	chr12:120793461..120795672-chr12:120885459..120888089,2	K562	blood:
15	chr12:120794136..120796708-chr12:120889639..120892127,2	MCF-7	breast:
16	chr12:120793489..120796080-chr12:120905908..120908643,2	K562	blood:
17	chr12:120792865..120795825-chr12:120869498..120872435,2	MCF-7	breast:
18	chr12:120794102..120795512-chr12:120867918..120868932,17	MCF-7	breast:
19	chr12:120794156..120794965-chr12:120867970..120868878,5	MCF-7	breast:
20	chr12:120791280..120792864-chr12:120793145..120794994,2	MCF-7	breast:
21	chr12:120794096..120794745-chr12:120877611..120878112,2	K562	blood:
22	chr12:120794376..120796521-chr12:120877642..120880151,3	MCF-7	breast:
23	chr12:120794600..120796834-chr12:120804822..120806971,2	K562	blood:
24	chr12:120794486..120796567-chr12:120881836..120883706,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000135097	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000111786	Chromatin interaction
ENSG00000111780	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000111775	Chromatin interaction
ENSG00000170855	Chromatin interaction
ENSG00000088986	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1007469	0.83[CHB][hapmap]
rs1076205	0.88[CEU][hapmap]
rs1076206	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1179430	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1179433	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1179434	0.87[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1179436	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1179437	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1179438	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1179440	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1179442	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1179443	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1179445	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1179446	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1179447	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1179449	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1179450	0.81[JPT][hapmap]
rs1183783	0.82[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1184532	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1306624	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs206948	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs206949	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs206952	0.91[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2261612	0.91[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs2283367	0.96[ASN][1000 genomes]
rs2285679	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2522131	0.88[EUR][1000 genomes]
rs2522133	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs2522134	0.81[ASW][hapmap];0.91[CEU][hapmap];0.87[LWK][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.80[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2951690	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3782901	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs735382	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7484571	0.85[ASN][1000 genomes]
rs757122	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs916842	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
2	nsv1047447	chr12:120645330-120808621	Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1179441	FBXO21	cis	parietal	SCAN
rs1179441	POP5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120764000-120799200	Weak transcription	Right Atrium	heart
2	chr12:120779400-120796800	Strong transcription	Brain Germinal Matrix	brain
3	chr12:120779600-120799000	Weak transcription	Fetal Heart	heart
4	chr12:120779800-120797400	Strong transcription	Fetal Brain Female	brain
5	chr12:120779800-120798800	Strong transcription	Fetal Intestine Small	intestine
6	chr12:120780400-120797600	Strong transcription	Fetal Stomach	stomach
7	chr12:120780800-120803200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr12:120781000-120796000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr12:120781000-120796200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:120781000-120796800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr12:120781200-120796000	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr12:120781200-120796600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:120781200-120796800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:120781400-120796600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:120783800-120799000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr12:120784800-120800400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr12:120786000-120796200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr12:120786200-120796000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr12:120787200-120796200	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:120789400-120799000	Weak transcription	Pancreas	Pancrea
21	chr12:120789400-120799000	Weak transcription	Stomach Mucosa	stomach
22	chr12:120789400-120799200	Weak transcription	Right Ventricle	heart
23	chr12:120789400-120802000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr12:120790200-120797000	Strong transcription	Fetal Muscle Trunk	muscle
25	chr12:120791000-120796600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr12:120791600-120795600	Weak transcription	Fetal Lung	lung
27	chr12:120793200-120795800	Strong transcription	H9 Cell Line	embryonic stem cell
28	chr12:120793200-120796600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:120793200-120797400	Strong transcription	Duodenum Mucosa	Duodenum
30	chr12:120793600-120795400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr12:120793600-120796000	Strong transcription	Fetal Muscle Leg	muscle
32	chr12:120794200-120794800	Enhancers	Brain Substantia Nigra	brain
33	chr12:120794200-120795200	Genic enhancers	Fetal Brain Male	brain
34	chr12:120794200-120796200	Strong transcription	Fetal Kidney	kidney
35	chr12:120794200-120799000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:120794400-120794800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:120794400-120794800	Enhancers	Spleen	Spleen
38	chr12:120794400-120795000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr12:120794400-120795200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:120794400-120795200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr12:120794600-120794800	Genic enhancers	HUES48 Cell Line	embryonic stem cell
42	chr12:120794600-120794800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr12:120794600-120794800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:120794600-120794800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:120794600-120794800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
46	chr12:120794600-120794800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
47	chr12:120794600-120794800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr12:120794600-120794800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr12:120794600-120794800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr12:120794600-120794800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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