Variant report

Variant	rs1179446
Chromosome Location	chr12:120797128-120797129
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:120795878..120797217-chr12:120867920..120868855,13	MCF-7	breast:
2	chr12:120729782..120731469-chr12:120795055..120797788,2	MCF-7	breast:
3	chr12:120791338..120793664-chr12:120794965..120797552,2	K562	blood:
4	chr12:120796844..120799038-chr12:120810328..120813184,2	K562	blood:

Variant related genes	Relation type
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]
rs1076206	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1179430	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1179433	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1179434	0.91[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1179436	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1179437	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1179438	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1179440	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1179441	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]
rs1179442	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]
rs1179443	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1179445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1179447	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1179449	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1179450	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs1183783	0.82[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1184532	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1306624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs206948	0.88[EUR][1000 genomes];0.83[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];0.91[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2261612	0.91[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs2283367	0.97[ASN][1000 genomes]
rs2285679	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2522131	0.87[EUR][1000 genomes]
rs2522133	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs2522134	0.81[ASW][hapmap];0.91[CEU][hapmap];0.84[LWK][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs2951690	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3782901	1.00[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];0.97[ASN][1000 genomes]
rs7484571	0.83[ASN][1000 genomes]
rs757122	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs916842	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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
rs1179446	FBXO21	cis	parietal	SCAN
rs1179446	POP5	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	chr12:120779600-120799000	Weak transcription	Fetal Heart	heart
3	chr12:120779800-120797400	Strong transcription	Fetal Brain Female	brain
4	chr12:120779800-120798800	Strong transcription	Fetal Intestine Small	intestine
5	chr12:120780400-120797600	Strong transcription	Fetal Stomach	stomach
6	chr12:120780800-120803200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr12:120783800-120799000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:120784800-120800400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr12:120789400-120799000	Weak transcription	Pancreas	Pancrea
10	chr12:120789400-120799000	Weak transcription	Stomach Mucosa	stomach
11	chr12:120789400-120799200	Weak transcription	Right Ventricle	heart
12	chr12:120789400-120802000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr12:120793200-120797400	Strong transcription	Duodenum Mucosa	Duodenum
14	chr12:120794200-120799000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:120794600-120797400	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr12:120794600-120797600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:120794600-120799000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
18	chr12:120794600-120799800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr12:120794800-120797400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr12:120794800-120797600	Strong transcription	Fetal Intestine Large	intestine
21	chr12:120794800-120798800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr12:120794800-120799000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:120794800-120799000	Weak transcription	Brain Angular Gyrus	brain
24	chr12:120794800-120799000	Weak transcription	Brain Hippocampus Middle	brain
25	chr12:120794800-120799000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr12:120794800-120799200	Weak transcription	Left Ventricle	heart
27	chr12:120794800-120799400	Weak transcription	Esophagus	oesophagus
28	chr12:120794800-120799800	Weak transcription	Brain Substantia Nigra	brain
29	chr12:120794800-120800200	Weak transcription	Gastric	stomach
30	chr12:120795000-120799000	Weak transcription	Osteobl	bone
31	chr12:120795200-120798400	Weak transcription	Fetal Brain Male	brain
32	chr12:120795200-120798600	Weak transcription	Brain Anterior Caudate	brain
33	chr12:120795200-120799000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:120795200-120799000	Weak transcription	NH-A	brain
35	chr12:120795400-120798800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr12:120795800-120797600	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr12:120795800-120798800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr12:120795800-120804200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr12:120796000-120797200	Genic enhancers	HUES48 Cell Line	embryonic stem cell
40	chr12:120796000-120797600	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr12:120796000-120798800	Genic enhancers	H1 Cell Line	embryonic stem cell
42	chr12:120796000-120799000	Weak transcription	Fetal Muscle Leg	muscle
43	chr12:120796200-120797400	Genic enhancers	HUES64 Cell Line	embryonic stem cell
44	chr12:120796200-120798800	Weak transcription	Fetal Lung	lung
45	chr12:120796200-120800000	Weak transcription	Fetal Kidney	kidney
46	chr12:120796200-120805000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:120796400-120797400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr12:120796400-120798200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr12:120796600-120797200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr12:120796600-120798800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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