Variant report

Variant	rs2271194
Chromosome Location	chr12:56477694-56477695
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56476793-56478634	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:56477360-56477731	HepG2	liver:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56435284..56441183-chr12:56476886..56481327,8	MCF-7	breast:
2	chr12:56471198..56482935-chr12:56506922..56516262,73	MCF-7	breast:
3	chr12:56475818..56478694-chr12:56550865..56553540,2	MCF-7	breast:
4	chr12:56471261..56483436-chr12:56494778..56506435,58	MCF-7	breast:
5	chr12:56472197..56476808-chr12:56477200..56483474,8	K562	blood:
6	chr12:56401139..56403498-chr12:56475848..56478502,3	K562	blood:
7	chr12:56472058..56475455-chr12:56477194..56480758,7	K562	blood:
8	chr12:56470948..56480058-chr12:56507665..56513741,17	K562	blood:
9	chr12:56391052..56392634-chr12:56475715..56477967,2	MCF-7	breast:

No data

Variant related genes	Relation type
ERBB3	TF binding region
ENSG00000196465	Chromatin interaction
ENSG00000170515	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000257411	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000257553	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000257449	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10876864	0.84[CEU][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes]
rs10876870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11171739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1131017	0.92[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs1701704	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs2292239	0.89[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2456973	0.94[JPT][hapmap]
rs2640562	0.90[ASN][1000 genomes]
rs3741499	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4759229	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs705696	1.00[ASN][1000 genomes]
rs705704	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs7297175	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7305461	0.82[JPT][hapmap]
rs7312770	0.88[ASN][1000 genomes]
rs772921	0.94[JPT][hapmap]
rs773109	0.83[JPT][hapmap]
rs7971751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs877636	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2271194	SUOX	cis	Thyroid	GTEx
rs2271194	RAB5B	cis	Muscle Skeletal	GTEx
rs2271194	DEFB124	trans	lymphoblastoid	RTeQTL
rs2271194	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL
rs2271194	RPS26///RPS26L///LOC644166///LOC644191	cis	uninvolved skin	skin_eQTL
rs2271194	RPS26///RPS26L///LOC644166///LOC644191	cis	lesional skin	skin_eQTL
rs2271194	AC034102.1	cis	Muscle Skeletal	GTEx
rs2271194	RPS26	cis	multi-tissue	Pritchard

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56474400-56497200	Weak transcription	Right Atrium	heart
2	chr12:56474600-56478800	Weak transcription	Left Ventricle	heart
3	chr12:56474800-56477800	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
4	chr12:56474800-56479800	Weak transcription	HMEC	breast
5	chr12:56475000-56485600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr12:56475200-56478800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:56475800-56479200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:56475800-56482400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:56476000-56477800	Enhancers	Placenta	Placenta
10	chr12:56476000-56480000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:56476000-56481000	Weak transcription	Spleen	Spleen
12	chr12:56476000-56481800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:56476200-56477800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr12:56476200-56478000	Transcr. at gene 5' and 3'	HepG2	liver
15	chr12:56476200-56497200	Weak transcription	Fetal Kidney	kidney
16	chr12:56476400-56478400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:56476400-56480000	Weak transcription	Fetal Heart	heart
18	chr12:56476400-56480200	Weak transcription	Hela-S3	cervix
19	chr12:56476400-56483200	Strong transcription	H9 Cell Line	embryonic stem cell
20	chr12:56476600-56478000	Enhancers	Colonic Mucosa	Colon
21	chr12:56476600-56478800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr12:56476600-56479200	Genic enhancers	Fetal Muscle Leg	muscle
23	chr12:56476600-56480400	Weak transcription	A549	lung
24	chr12:56476600-56487400	Weak transcription	Lung	lung
25	chr12:56476600-56496400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr12:56476600-56497600	Weak transcription	Small Intestine	intestine
27	chr12:56476800-56477800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr12:56476800-56478600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr12:56476800-56479000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr12:56476800-56479800	Weak transcription	HSMMtube	muscle
31	chr12:56476800-56487200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr12:56477000-56479800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr12:56477000-56497000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:56477000-56497000	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr12:56477200-56477800	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
36	chr12:56477200-56477800	Transcr. at gene 5' and 3'	Fetal Intestine Large	intestine
37	chr12:56477200-56478800	Weak transcription	K562	blood
38	chr12:56477200-56481600	Genic enhancers	Rectal Mucosa Donor 31	rectum
39	chr12:56477400-56477800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr12:56477400-56477800	Transcr. at gene 5' and 3'	Liver	Liver
41	chr12:56477400-56477800	Flanking Active TSS	Brain Cingulate Gyrus	brain
42	chr12:56477400-56477800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:56477400-56477800	Flanking Active TSS	Brain Substantia Nigra	brain
44	chr12:56477400-56477800	Strong transcription	Placenta Amnion	Placenta Amnion
45	chr12:56477400-56477800	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
46	chr12:56477400-56477800	Strong transcription	Rectal Smooth Muscle	rectum
47	chr12:56477400-56477800	Strong transcription	NHEK	skin
48	chr12:56477400-56478000	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr12:56477400-56478000	Flanking Active TSS	Brain Anterior Caudate	brain
50	chr12:56477400-56478000	Transcr. at gene 5' and 3'	Brain Hippocampus Middle	brain

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