Variant report

Variant	rs1179442
Chromosome Location	chr12:120796112-120796113
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:120795878..120797217-chr12:120867920..120868855,13	MCF-7	breast:
2	chr12:120795626..120796658-chr12:120867925..120868925,7	MCF-7	breast:
3	chr12:120794931..120796689-chr12:120831287..120834141,2	MCF-7	breast:
4	chr12:120793772..120796303-chr12:120865942..120868774,2	MCF-7	breast:
5	chr12:120793158..120796166-chr12:120882003..120884232,3	K562	blood:
6	chr12:120794499..120796527-chr12:120866923..120868493,2	K562	blood:
7	chr12:120729782..120731469-chr12:120795055..120797788,2	MCF-7	breast:
8	chr12:120666353..120667903-chr12:120793999..120796397,2	MCF-7	breast:
9	chr12:120794136..120796708-chr12:120889639..120892127,2	MCF-7	breast:
10	chr12:120791338..120793664-chr12:120794965..120797552,2	K562	blood:
11	chr12:120794376..120796521-chr12:120877642..120880151,3	MCF-7	breast:
12	chr12:120794600..120796834-chr12:120804822..120806971,2	K562	blood:
13	chr12:120794486..120796567-chr12:120881836..120883706,2	MCF-7	breast:
14	chr12:120795985..120796800-chr12:120804726..120805531,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000170855	Chromatin interaction
ENSG00000135097	Chromatin interaction
ENSG00000111775	Chromatin interaction
ENSG00000200795	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1076205	0.88[CEU][hapmap];0.81[YRI][hapmap]
rs1076206	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1179430	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1179433	0.83[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];0.85[ASN][1000 genomes]
rs1179436	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1179437	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1179438	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1179440	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1179441	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	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1179445	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1179447	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1179449	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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];0.85[ASN][1000 genomes]
rs1306624	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs206948	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs206949	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs206952	0.91[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2261612	0.91[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs2283367	0.97[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];0.90[LWK][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];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];0.97[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];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs916842	0.89[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
rs1179442	POP5	cis	parietal	SCAN
rs1179442	FBXO21	cis	parietal	SCAN

Chromatin state (count:62 , 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	chr12:120781000-120796200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:120781000-120796800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr12:120781200-120796600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:120781200-120796800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:120781400-120796600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:120783800-120799000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr12:120784800-120800400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr12:120786000-120796200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr12:120787200-120796200	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:120789400-120799000	Weak transcription	Pancreas	Pancrea
18	chr12:120789400-120799000	Weak transcription	Stomach Mucosa	stomach
19	chr12:120789400-120799200	Weak transcription	Right Ventricle	heart
20	chr12:120789400-120802000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr12:120790200-120797000	Strong transcription	Fetal Muscle Trunk	muscle
22	chr12:120791000-120796600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr12:120793200-120796600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:120793200-120797400	Strong transcription	Duodenum Mucosa	Duodenum
25	chr12:120794200-120796200	Strong transcription	Fetal Kidney	kidney
26	chr12:120794200-120799000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:120794600-120796800	Enhancers	Placenta	Placenta
28	chr12:120794600-120797400	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:120794600-120797600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:120794600-120799000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
31	chr12:120794600-120799800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:120794800-120796400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr12:120794800-120797400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr12:120794800-120797600	Strong transcription	Fetal Intestine Large	intestine
35	chr12:120794800-120798800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr12:120794800-120799000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:120794800-120799000	Weak transcription	Brain Angular Gyrus	brain
38	chr12:120794800-120799000	Weak transcription	Brain Hippocampus Middle	brain
39	chr12:120794800-120799000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr12:120794800-120799200	Weak transcription	Left Ventricle	heart
41	chr12:120794800-120799400	Weak transcription	Esophagus	oesophagus
42	chr12:120794800-120799800	Weak transcription	Brain Substantia Nigra	brain
43	chr12:120794800-120800200	Weak transcription	Gastric	stomach
44	chr12:120795000-120796800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:120795000-120799000	Weak transcription	Osteobl	bone
46	chr12:120795200-120796400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:120795200-120798400	Weak transcription	Fetal Brain Male	brain
48	chr12:120795200-120798600	Weak transcription	Brain Anterior Caudate	brain
49	chr12:120795200-120799000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr12:120795200-120799000	Weak transcription	NH-A	brain

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