Variant report

Variant	rs1633359
Chromosome Location	chr12:58122876-58122877
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58108037..58111841-chr12:58122870..58126206,3	K562	blood:
2	chr12:57856178..57857976-chr12:58122107..58124525,2	K562	blood:
3	chr12:58085694..58088995-chr12:58116929..58123534,7	MCF-7	breast:
4	chr12:57911913..57914667-chr12:58122854..58126849,5	K562	blood:
5	chr12:57984952..57986609-chr12:58120823..58123199,2	K562	blood:
6	chr12:58085407..58089363-chr12:58117669..58123604,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000208028	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000111087	Chromatin interaction
ENSG00000135506	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000166908	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1050045	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12826708	0.82[AMR][1000 genomes]
rs12826985	0.82[AMR][1000 genomes]
rs17852479	0.80[AMR][1000 genomes]
rs2270777	0.82[AMR][1000 genomes]
rs238517	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs701007	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7138608	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7295422	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7311632	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7952989	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs799265	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs799267	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	esv1851618	chr12:58109302-58131947	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv559045	chr12:58112189-58165085	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv470296	chr12:58112189-58177292	Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
7	nsv826383	chr12:58118080-58123647	Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv899122	chr12:58118248-58137563	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv899123	chr12:58118248-58155023	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1633359	OS9	cis	Esophagus Muscularis	GTEx
rs1633359	XRCC6BP1	cis	Artery Tibial	GTEx
rs1633359	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs1633359	XRCC6BP1	cis	Muscle Skeletal	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58115200-58123600	Weak transcription	GM12878-XiMat	blood
2	chr12:58115600-58124000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr12:58118400-58132000	Strong transcription	Primary T cells from cord blood	blood
4	chr12:58119200-58132000	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr12:58119600-58130400	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr12:58119600-58130400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:58119600-58131200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr12:58119600-58131400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:58119600-58132400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr12:58119600-58132800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr12:58119600-58133000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:58119800-58128000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:58119800-58128600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr12:58120000-58129000	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr12:58120000-58131400	Strong transcription	Primary B cells from peripheral blood	blood
16	chr12:58120200-58129000	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr12:58120200-58130200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:58120400-58131800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:58120400-58132400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:58120600-58129200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
21	chr12:58120800-58128800	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr12:58120800-58129200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr12:58121000-58124000	Weak transcription	HSMMtube	muscle
24	chr12:58121000-58129200	Strong transcription	Primary B cells from cord blood	blood
25	chr12:58121200-58124200	Weak transcription	A549	lung
26	chr12:58121200-58126800	Weak transcription	Brain Angular Gyrus	brain
27	chr12:58121200-58128000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:58121400-58124800	Weak transcription	Liver	Liver
29	chr12:58121400-58125200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr12:58121400-58132800	Strong transcription	Thymus	Thymus
31	chr12:58121600-58123200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:58121600-58125400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr12:58121600-58126000	Weak transcription	Brain Hippocampus Middle	brain
34	chr12:58121600-58126400	Weak transcription	Brain Anterior Caudate	brain
35	chr12:58121600-58130200	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr12:58121800-58123000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:58121800-58123800	Weak transcription	Esophagus	oesophagus
38	chr12:58121800-58124000	Weak transcription	NHLF	lung
39	chr12:58121800-58125000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr12:58121800-58125400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr12:58121800-58129400	Strong transcription	Spleen	Spleen
42	chr12:58121800-58130200	Weak transcription	Gastric	stomach
43	chr12:58121800-58132400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr12:58122000-58123400	Weak transcription	Dnd41	blood
45	chr12:58122000-58124400	Weak transcription	Right Ventricle	heart
46	chr12:58122000-58129400	Weak transcription	Lung	lung
47	chr12:58122200-58123000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr12:58122200-58123000	Weak transcription	Fetal Thymus	thymus
49	chr12:58122200-58123200	Weak transcription	Fetal Brain Female	brain
50	chr12:58122400-58124000	Weak transcription	Rectal Mucosa Donor 29	rectum

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