Variant report

Variant	rs34273234
Chromosome Location	chr12:56372021-56372022
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56371193-56372090	HL-60	blood:	n/a	n/a
2	POLR2A	chr12:56371436-56372092	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56365739..56372949-chr12:56384756..56392202,12	MCF-7	breast:
2	chr12:56320862..56327055-chr12:56370927..56377943,9	MCF-7	breast:
3	chr12:56364512..56372057-chr12:56434108..56438254,11	MCF-7	breast:
4	chr12:56370164..56372810-chr12:56390146..56392371,2	MCF-7	breast:

Variant related genes	Relation type
PMEL	TF binding region
ENSG00000197728	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000255990	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000065357	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1045435	0.96[EUR][1000 genomes]
rs11171713	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11171714	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11171715	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11550558	0.92[EUR][1000 genomes]
rs12099979	0.81[AMR][1000 genomes]
rs12815302	0.87[AMR][1000 genomes]
rs12815488	0.87[AMR][1000 genomes]
rs12817765	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12831468	0.87[AMR][1000 genomes]
rs17118206	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17118208	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17118262	0.87[AMR][1000 genomes]
rs34071823	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34228181	0.81[AMR][1000 genomes]
rs34303864	0.87[AMR][1000 genomes]
rs34962186	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67594137	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71447768	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71459326	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71459327	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71459334	0.87[AMR][1000 genomes]
rs71459339	0.81[AMR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs34273234	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL
rs34273234	SUOX	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56368600-56374200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:56368600-56375400	Weak transcription	Lung	lung
3	chr12:56368600-56383200	Weak transcription	Gastric	stomach
4	chr12:56368800-56374200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:56368800-56379000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:56369000-56372400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr12:56369000-56373000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:56369000-56373000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:56369000-56374000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr12:56369000-56383600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:56369200-56372800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr12:56369200-56373000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:56369200-56373000	Weak transcription	NH-A	brain
14	chr12:56369200-56374000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr12:56369200-56374000	Weak transcription	HSMMtube	muscle
16	chr12:56369200-56374200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr12:56369200-56375000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:56369200-56375200	Weak transcription	A549	lung
19	chr12:56369200-56376200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr12:56369200-56376200	Weak transcription	NHDF-Ad	bronchial
21	chr12:56369200-56379000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr12:56369200-56380000	Weak transcription	Right Ventricle	heart
23	chr12:56369200-56380400	Weak transcription	Aorta	Aorta
24	chr12:56369200-56383600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr12:56369200-56384600	Weak transcription	Psoas Muscle	Psoas
26	chr12:56369400-56372600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:56369400-56372800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr12:56369400-56372800	Weak transcription	Fetal Intestine Large	intestine
29	chr12:56369400-56372800	Weak transcription	Hela-S3	cervix
30	chr12:56369400-56373000	Weak transcription	Primary B cells from peripheral blood	blood
31	chr12:56369400-56373000	Weak transcription	Brain Anterior Caudate	brain
32	chr12:56369400-56373000	Weak transcription	Brain Germinal Matrix	brain
33	chr12:56369400-56373400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:56369400-56374200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr12:56369400-56374200	Weak transcription	Esophagus	oesophagus
36	chr12:56369400-56374200	Weak transcription	Spleen	Spleen
37	chr12:56369400-56374400	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr12:56369400-56375200	Weak transcription	Fetal Brain Female	brain
39	chr12:56369400-56375200	Weak transcription	Fetal Kidney	kidney
40	chr12:56369400-56379400	Strong transcription	Fetal Muscle Leg	muscle
41	chr12:56369400-56381000	Weak transcription	Small Intestine	intestine
42	chr12:56369400-56383400	Weak transcription	Pancreas	Pancrea
43	chr12:56369400-56384200	Weak transcription	Fetal Brain Male	brain
44	chr12:56369400-56389400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:56369600-56372400	Weak transcription	Placenta	Placenta
46	chr12:56369600-56373200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr12:56369800-56372400	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr12:56369800-56389600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:56370000-56375200	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr12:56370000-56376400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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