Variant report

Variant	rs34485293
Chromosome Location	chr12:56422162-56422163
allele	A/C
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56421691..56428762-chr12:56433229..56437460,13	MCF-7	breast:
2	chr12:56414513..56416676-chr12:56421694..56423557,2	K562	blood:
3	chr12:56387127..56392729-chr12:56419203..56425417,17	MCF-7	breast:
4	chr12:56421656..56424800-chr12:56509383..56513294,3	MCF-7	breast:
5	chr12:56400024..56405744-chr12:56418580..56425265,13	MCF-7	breast:
6	chr12:56387922..56391678-chr12:56420770..56424828,6	MCF-7	breast:
7	chr12:56419317..56422414-chr12:56434888..56438037,4	K562	blood:
8	chr12:56390476..56392959-chr12:56421317..56423015,2	K562	blood:
9	chr12:56417053..56422414-chr12:56432550..56437155,7	K562	blood:
10	chr12:56422020..56423685-chr12:56426127..56428274,2	K562	blood:
11	chr12:56350151..56351741-chr12:56420142..56422270,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257449	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000139641	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11171713	0.81[AMR][1000 genomes]
rs11171714	0.81[AMR][1000 genomes]
rs12099979	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12810011	0.91[EUR][1000 genomes]
rs12815302	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12815387	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12815488	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12817765	0.81[AMR][1000 genomes]
rs12818756	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12831468	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1614219	0.89[EUR][1000 genomes]
rs1689511	0.86[EUR][1000 genomes]
rs1701706	0.89[EUR][1000 genomes]
rs17118206	0.81[AMR][1000 genomes]
rs17118208	0.81[AMR][1000 genomes]
rs17118262	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2131569	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2456972	0.89[EUR][1000 genomes]
rs2658479	0.93[EUR][1000 genomes]
rs34071823	0.81[AMR][1000 genomes]
rs34228181	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34303864	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34406511	0.91[EUR][1000 genomes]
rs34507011	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34602183	0.87[EUR][1000 genomes]
rs34650555	0.91[EUR][1000 genomes]
rs34921584	0.91[EUR][1000 genomes]
rs34962186	0.81[AMR][1000 genomes]
rs35485002	0.95[EUR][1000 genomes]
rs35666826	0.80[EUR][1000 genomes]
rs35961650	0.93[EUR][1000 genomes]
rs4759022	0.91[EUR][1000 genomes]
rs4759239	0.93[EUR][1000 genomes]
rs71447768	0.81[AMR][1000 genomes]
rs71459326	0.81[AMR][1000 genomes]
rs71459327	0.81[AMR][1000 genomes]
rs71459334	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71459336	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71459339	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71459342	0.80[EUR][1000 genomes]
rs7298818	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7300772	0.89[EUR][1000 genomes]
rs772919	0.88[EUR][1000 genomes]
rs772922	0.89[EUR][1000 genomes]
rs772923	0.91[EUR][1000 genomes]
rs773115	0.86[EUR][1000 genomes]
rs7963590	0.80[EUR][1000 genomes]
rs7977537	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs34485293	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL
rs34485293	SUOX	cis	Thyroid	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56402200-56434800	Weak transcription	Psoas Muscle	Psoas
2	chr12:56402400-56422400	Weak transcription	Osteobl	bone
3	chr12:56402400-56423000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr12:56406000-56422800	Weak transcription	HSMM	muscle
5	chr12:56409400-56435000	Weak transcription	Stomach Mucosa	stomach
6	chr12:56409800-56422600	Weak transcription	Liver	Liver
7	chr12:56415400-56422400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:56415600-56426200	Weak transcription	Aorta	Aorta
9	chr12:56415800-56422400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:56415800-56422400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:56416000-56422800	Weak transcription	NH-A	brain
12	chr12:56416000-56426000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr12:56416000-56434800	Weak transcription	Primary B cells from cord blood	blood
14	chr12:56416000-56434800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr12:56416000-56435000	Weak transcription	Right Atrium	heart
16	chr12:56416200-56422600	Weak transcription	NHDF-Ad	bronchial
17	chr12:56416200-56425800	Weak transcription	Small Intestine	intestine
18	chr12:56416200-56426000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr12:56416200-56426000	Weak transcription	Colonic Mucosa	Colon
20	chr12:56416200-56434800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr12:56416400-56431000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr12:56416600-56422800	Weak transcription	HepG2	liver
23	chr12:56416600-56431000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr12:56417400-56430800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:56417600-56422200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr12:56417800-56423200	Strong transcription	Brain Inferior Temporal Lobe	brain
27	chr12:56417800-56430600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:56418000-56423600	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr12:56418000-56425400	Weak transcription	Fetal Brain Male	brain
30	chr12:56418000-56431000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:56418200-56423400	Strong transcription	Brain Anterior Caudate	brain
32	chr12:56418200-56423800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:56418200-56423800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:56418200-56427200	Strong transcription	K562	blood
35	chr12:56418200-56432600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:56418400-56422600	Strong transcription	Fetal Intestine Large	intestine
37	chr12:56418400-56422600	Strong transcription	Fetal Thymus	thymus
38	chr12:56418400-56422800	Strong transcription	Fetal Intestine Small	intestine
39	chr12:56418400-56423000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:56418400-56423000	Strong transcription	Brain Cingulate Gyrus	brain
41	chr12:56418400-56423200	Strong transcription	Ovary	ovary
42	chr12:56418400-56423600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr12:56418400-56423800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr12:56418400-56424000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr12:56418400-56424000	Strong transcription	Dnd41	blood
46	chr12:56418400-56424200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:56418400-56432000	Strong transcription	Brain Germinal Matrix	brain
48	chr12:56418400-56432800	Strong transcription	Fetal Brain Female	brain
49	chr12:56418400-56433000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:56418600-56422400	Strong transcription	Fetal Muscle Trunk	muscle

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