Variant report

Variant	rs773108
Chromosome Location	chr12:56369911-56369912
allele	A/G
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:56363397..56371565-chr12:56432514..56437993,13	K562	blood:
2	chr12:56365739..56372949-chr12:56384756..56392202,12	MCF-7	breast:
3	chr12:56365214..56370075-chr12:56508797..56513405,7	K562	blood:
4	chr12:56364726..56370308-chr12:56432734..56438629,15	K562	blood:
5	chr12:56364512..56372057-chr12:56434108..56438254,11	MCF-7	breast:
6	chr12:56318492..56327488-chr12:56364288..56371675,16	MCF-7	breast:
7	chr12:56209486..56213209-chr12:56366653..56370251,5	MCF-7	breast:
8	chr12:56210044..56216553-chr12:56364276..56371676,13	MCF-7	breast:
9	chr12:56364761..56370418-chr12:56496365..56499534,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000197728	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000255990	Chromatin interaction
ENSG00000257390	Chromatin interaction
ENSG00000205323	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000170515	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1081975	0.83[ASN][1000 genomes]
rs10876864	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs1131017	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs1689510	0.83[EUR][1000 genomes]
rs1701704	0.90[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.92[TSI][hapmap]
rs1873914	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2048036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2069408	0.95[CHB][hapmap];0.82[YRI][hapmap]
rs2069415	1.00[YRI][hapmap]
rs2456973	0.90[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap]
rs61937247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61937248	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61937249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs705698	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs705699	1.00[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs705700	0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs705702	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs705704	0.90[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.92[TSI][hapmap]
rs772920	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs772921	0.90[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs773107	0.95[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs773109	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs773110	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773111	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773112	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs773114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[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	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs773108	SUOX	cis	Nerve Tibial	GTEx
rs773108	DNAJC14	cis	parietal	SCAN
rs773108	CSRNP2	cis	parietal	SCAN
rs773108	SUOX	cis	lung	GTEx
rs773108	RPS26///RPS26L///LOC644166///LOC644191	cis	uninvolved skin	skin_eQTL
rs773108	AC034102.1	cis	Muscle Skeletal	GTEx
rs773108	TAC3	cis	parietal	SCAN
rs773108	SUOX	cis	cerebellum	SCAN
rs773108	SUOX	cis	Thyroid	GTEx
rs773108	SUOX	cis	parietal	SCAN
rs773108	RAB5B	cis	Muscle Skeletal	GTEx
rs773108	RPS26	cis	lymphoblastoid	seeQTL
rs773108	RPS26///RPS26L///LOC644166///LOC644191	cis	lesional skin	skin_eQTL
rs773108	RPS26	cis	multi-tissue	Pritchard
rs773108	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL
rs773108	DEFB124	trans	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56367000-56370000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:56368600-56370200	Weak transcription	Stomach Mucosa	stomach
3	chr12:56368600-56371000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:56368600-56371600	Enhancers	Fetal Heart	heart
5	chr12:56368600-56374200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:56368600-56375400	Weak transcription	Lung	lung
7	chr12:56368600-56383200	Weak transcription	Gastric	stomach
8	chr12:56368800-56374200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:56368800-56379000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:56369000-56370000	Enhancers	Primary T cells from cord blood	blood
11	chr12:56369000-56370000	Weak transcription	HSMM	muscle
12	chr12:56369000-56370000	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr12:56369000-56370200	Weak transcription	Right Atrium	heart
14	chr12:56369000-56370400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:56369000-56370600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr12:56369000-56370600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr12:56369000-56370600	Enhancers	Rectal Smooth Muscle	rectum
18	chr12:56369000-56370600	Enhancers	HepG2	liver
19	chr12:56369000-56371000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr12:56369000-56372000	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr12:56369000-56372400	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr12:56369000-56373000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr12:56369000-56373000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr12:56369000-56374000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr12:56369000-56383600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr12:56369200-56370000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:56369200-56370000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr12:56369200-56370000	Enhancers	Brain Hippocampus Middle	brain
29	chr12:56369200-56370000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr12:56369200-56370000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr12:56369200-56370000	Weak transcription	GM12878-XiMat	blood
32	chr12:56369200-56370000	Weak transcription	K562	blood
33	chr12:56369200-56370000	Weak transcription	NHLF	lung
34	chr12:56369200-56370000	Weak transcription	Osteobl	bone
35	chr12:56369200-56370200	Weak transcription	Colon Smooth Muscle	Colon
36	chr12:56369200-56370400	Enhancers	Adipose Nuclei	Adipose
37	chr12:56369200-56370400	Enhancers	Brain Angular Gyrus	brain
38	chr12:56369200-56370400	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr12:56369200-56370600	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr12:56369200-56370600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
41	chr12:56369200-56370600	Weak transcription	Fetal Intestine Small	intestine
42	chr12:56369200-56370600	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr12:56369200-56370600	Weak transcription	Fetal Stomach	stomach
44	chr12:56369200-56370600	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr12:56369200-56370600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr12:56369200-56370800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr12:56369200-56370800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr12:56369200-56370800	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr12:56369200-56370800	Enhancers	Brain Substantia Nigra	brain
50	chr12:56369200-56371000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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