Variant report

Variant	rs2069408
Chromosome Location	chr12:56364321-56364322
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56364246-56364783	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:56364316-56364861	K562	blood:	n/a	n/a
3	POLR2A	chr12:56364303-56365056	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr12:56364249-56369472	IMR90	lung:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:56363397..56371565-chr12:56432514..56437993,13	K562	blood:
2	chr12:56364150..56366741-chr7:2393948..2395853,2	MCF-7	breast:
3	chr12:56364085..56366217-chr12:56434598..56438715,3	MCF-7	breast:
4	chr12:56332717..56336094-chr12:56364167..56367444,3	K562	blood:
5	chr12:56318132..56330507-chr12:56363672..56369798,22	MCF-7	breast:
6	chr12:56364281..56367939-chr12:56391027..56393496,3	K562	blood:
7	chr12:56364310..56368149-chr12:56508797..56512267,4	K562	blood:
8	chr12:56362691..56364753-chr12:56492811..56495161,2	K562	blood:
9	chr12:56362871..56364397-chr12:56400894..56402474,2	MCF-7	breast:
10	chr12:56362653..56364406-chr12:56435895..56438627,2	K562	blood:
11	chr12:56318492..56327488-chr12:56364288..56371675,16	MCF-7	breast:
12	chr12:56121691..56123442-chr12:56362303..56365050,2	MCF-7	breast:
13	chr12:56363280..56366159-chr12:56473026..56475603,2	MCF-7	breast:
14	chr12:56210044..56216553-chr12:56364276..56371676,13	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000258554	TF binding region
CDK2	TF binding region
PMEL	TF binding region
RAB5B	TF binding region
ENSG00000065361	Chromatin interaction
ENSG00000258056	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000257411	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000106263	Chromatin interaction
ENSG00000205323	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000106266	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000257390	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10876864	0.84[CHB][hapmap]
rs1873914	0.95[CHB][hapmap]
rs2048036	0.80[ASN][1000 genomes]
rs2069415	0.82[YRI][hapmap]
rs61937247	0.80[ASN][1000 genomes]
rs61937248	0.80[ASN][1000 genomes]
rs61937249	0.80[ASN][1000 genomes]
rs705698	0.89[CHB][hapmap];0.82[YRI][hapmap]
rs705699	0.95[CHB][hapmap]
rs705700	0.89[CHB][hapmap]
rs705702	0.89[CHB][hapmap];0.82[YRI][hapmap]
rs772921	0.84[CHB][hapmap]
rs773108	0.95[CHB][hapmap];0.82[YRI][hapmap]
rs773109	0.95[CHB][hapmap];0.82[YRI][hapmap]
rs773114	0.95[CHB][hapmap]

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

Variant related diseases (count:1)

Disease	PMID	Source
Asthma	21804548	GWAS catalog

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs2069408	SUOX	cis	Thyroid	GTEx
rs2069408	LOC441502	trans	multi-tissue	Pritchard
rs2069408	MADCAM1	trans	multi-tissue	Pritchard
rs2069408	LOC644934	trans	multi-tissue	Pritchard
rs2069408	RPS26	cis	lymphoblastoid	seeQTL
rs2069408	RPS26	cis	multi-tissue	Pritchard
rs2069408	SUOX	cis	lung	GTEx
rs2069408	DNAJC14	cis	parietal	SCAN
rs2069408	CCDC4	trans	multi-tissue	Pritchard
rs2069408	RPS26	cis	brain	seeQTL
rs2069408	TSPAN31	cis	parietal	SCAN
rs2069408	MAGEC1	trans	multi-tissue	Pritchard
rs2069408	SUOX	cis	cerebellum	SCAN
rs2069408	SUOX	cis	parietal	SCAN
rs2069408	FLJ20280	trans	multi-tissue	Pritchard
rs2069408	AC034102.1	cis	Muscle Skeletal	GTEx
rs2069408	RAB5B	cis	Muscle Skeletal	GTEx
rs2069408	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL
rs2069408	BLOC1S1	cis	parietal	SCAN
rs2069408	CSRNP2	cis	parietal	SCAN
rs2069408	LOC441377	trans	multi-tissue	Pritchard
rs2069408	RPS26P10	trans	multi-tissue	Pritchard

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56361200-56365400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr12:56361200-56366800	Weak transcription	Aorta	Aorta
3	chr12:56361200-56367200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:56361400-56364400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:56361400-56365400	Weak transcription	HSMMtube	muscle
6	chr12:56361400-56366000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr12:56361400-56366000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr12:56361400-56366600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr12:56361400-56366600	Weak transcription	Brain Anterior Caudate	brain
10	chr12:56361400-56366600	Weak transcription	Left Ventricle	heart
11	chr12:56361400-56366600	Weak transcription	Psoas Muscle	Psoas
12	chr12:56361400-56366800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:56361600-56365600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:56361600-56366000	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr12:56361600-56366000	Weak transcription	Colonic Mucosa	Colon
16	chr12:56361600-56366000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr12:56361600-56366200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr12:56361600-56366200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr12:56361600-56366200	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr12:56361600-56366400	Weak transcription	Primary B cells from cord blood	blood
21	chr12:56361600-56366400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr12:56361600-56366600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr12:56361800-56364400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr12:56361800-56364400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr12:56361800-56364800	Weak transcription	Adipose Nuclei	Adipose
26	chr12:56361800-56364800	Weak transcription	Ovary	ovary
27	chr12:56361800-56364800	Weak transcription	A549	lung
28	chr12:56361800-56365600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:56361800-56365600	Weak transcription	Fetal Brain Female	brain
30	chr12:56361800-56365800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr12:56361800-56365800	Weak transcription	Colon Smooth Muscle	Colon
32	chr12:56361800-56365800	Weak transcription	Fetal Brain Male	brain
33	chr12:56361800-56366000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr12:56361800-56366000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:56361800-56366000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr12:56361800-56366000	Weak transcription	Brain Germinal Matrix	brain
37	chr12:56361800-56366000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr12:56361800-56366000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr12:56361800-56366000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr12:56361800-56366400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr12:56361800-56366600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr12:56361800-56366600	Weak transcription	Brain Substantia Nigra	brain
43	chr12:56361800-56366600	Weak transcription	Esophagus	oesophagus
44	chr12:56361800-56366600	Weak transcription	Pancreas	Pancrea
45	chr12:56361800-56366600	Weak transcription	Spleen	Spleen
46	chr12:56362000-56364400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr12:56362000-56364400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:56362000-56365200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr12:56362000-56365200	Weak transcription	NHDF-Ad	bronchial
50	chr12:56362000-56365800	Strong transcription	HUES64 Cell Line	embryonic stem cell

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