Variant report

Variant	rs35485002
Chromosome Location	chr12:56429575-56429576
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56366512..56369060-chr12:56428016..56430790,3	K562	blood:
2	chr12:56429367..56432151-chr12:56511297..56513264,2	K562	blood:
3	chr12:56427631..56431048-chr12:56433357..56437105,6	K562	blood:
4	chr12:56223341..56224931-chr12:56428312..56431174,2	MCF-7	breast:
5	chr12:56428161..56431029-chr12:56472610..56474694,3	MCF-7	breast:
6	chr12:56388425..56391424-chr12:56428602..56430718,2	K562	blood:

Variant related genes	Relation type
ENSG00000111540	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000185664	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11171713	0.81[AMR][1000 genomes]
rs11171714	0.81[AMR][1000 genomes]
rs12099979	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12810011	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12815302	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12815387	0.96[EUR][1000 genomes]
rs12815488	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12817471	0.81[EUR][1000 genomes]
rs12817765	0.81[AMR][1000 genomes]
rs12818756	0.96[EUR][1000 genomes]
rs12831468	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1614219	0.94[EUR][1000 genomes]
rs1689511	0.91[EUR][1000 genomes]
rs1701706	0.94[EUR][1000 genomes]
rs17118206	0.81[AMR][1000 genomes]
rs17118208	0.81[AMR][1000 genomes]
rs17118262	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2131569	0.96[EUR][1000 genomes]
rs2456972	0.94[EUR][1000 genomes]
rs2658479	0.98[EUR][1000 genomes]
rs34071823	0.81[AMR][1000 genomes]
rs34228181	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34303864	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34406511	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs34485293	0.95[EUR][1000 genomes]
rs34507011	0.94[EUR][1000 genomes]
rs34602183	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs34650555	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs34921584	0.92[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs34962186	0.81[AMR][1000 genomes]
rs35662491	0.82[EUR][1000 genomes]
rs35666826	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs35961650	0.98[EUR][1000 genomes]
rs4759022	0.96[EUR][1000 genomes]
rs4759239	0.98[EUR][1000 genomes]
rs71447768	0.81[AMR][1000 genomes]
rs71459326	0.81[AMR][1000 genomes]
rs71459327	0.81[AMR][1000 genomes]
rs71459334	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71459336	0.94[EUR][1000 genomes]
rs71459339	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71459342	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7298818	0.91[EUR][1000 genomes]
rs7300772	0.94[EUR][1000 genomes]
rs772919	0.93[EUR][1000 genomes]
rs772922	0.94[EUR][1000 genomes]
rs772923	0.96[EUR][1000 genomes]
rs773115	0.91[EUR][1000 genomes]
rs7963590	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7977537	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv1067906	chr12:56424828-56445284	Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs35485002	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL
rs35485002	SUOX	cis	Thyroid	GTEx
rs35485002	ENSG00000123411	cis	multi-tissue	Pritchard

Chromatin state (count:121 , 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	chr12:56409400-56435000	Weak transcription	Stomach Mucosa	stomach
3	chr12:56416000-56434800	Weak transcription	Primary B cells from cord blood	blood
4	chr12:56416000-56434800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr12:56416000-56435000	Weak transcription	Right Atrium	heart
6	chr12:56416200-56434800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:56416400-56431000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr12:56416600-56431000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr12:56417400-56430800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr12:56417800-56430600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:56418000-56431000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:56418200-56432600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:56418400-56432000	Strong transcription	Brain Germinal Matrix	brain
14	chr12:56418400-56432800	Strong transcription	Fetal Brain Female	brain
15	chr12:56418400-56433000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:56418600-56431400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr12:56418600-56433200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:56421200-56430000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr12:56421800-56434600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr12:56423000-56429800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr12:56423200-56429800	Strong transcription	Fetal Kidney	kidney
22	chr12:56423200-56431400	Strong transcription	Fetal Muscle Leg	muscle
23	chr12:56423200-56431600	Strong transcription	Fetal Muscle Trunk	muscle
24	chr12:56423400-56433000	Strong transcription	Fetal Intestine Large	intestine
25	chr12:56423600-56433400	Strong transcription	Fetal Stomach	stomach
26	chr12:56423600-56434400	Weak transcription	HMEC	breast
27	chr12:56423600-56434800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr12:56423600-56434800	Weak transcription	NH-A	brain
29	chr12:56423800-56433200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr12:56423800-56434000	Weak transcription	NHEK	skin
31	chr12:56424600-56432800	Strong transcription	Placenta	Placenta
32	chr12:56424600-56433200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:56424600-56433200	Strong transcription	Fetal Lung	lung
34	chr12:56425000-56430000	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr12:56425000-56430400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:56425000-56431400	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr12:56425000-56431600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:56425000-56431600	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr12:56425200-56430000	Strong transcription	Adipose Nuclei	Adipose
40	chr12:56425200-56430600	Strong transcription	Primary hematopoietic stem cells	blood
41	chr12:56425200-56430800	Strong transcription	Left Ventricle	heart
42	chr12:56425200-56431400	Strong transcription	Brain Angular Gyrus	brain
43	chr12:56425200-56432800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr12:56425400-56430000	Strong transcription	Fetal Brain Male	brain
45	chr12:56425400-56430600	Strong transcription	Brain Cingulate Gyrus	brain
46	chr12:56425400-56430800	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr12:56425400-56431600	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr12:56425600-56431400	Strong transcription	Brain Hippocampus Middle	brain
49	chr12:56425600-56431600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:56425600-56432600	Strong transcription	Brain Anterior Caudate	brain

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