Variant report

Variant	rs7512893
Chromosome Location	chr1:77880168-77880169
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	JUN	chr1:77880129-77880329	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:77879822..77883300-chr1:77884323..77886627,3	K562	blood:

Variant related genes	Relation type
AK5	TF binding region
ENSG00000251767	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10493605	0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs10873937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131772	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498404	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1532507	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17100524	0.82[ASN][1000 genomes]
rs34277277	0.98[ASN][1000 genomes]
rs3844166	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs72681629	0.84[ASN][1000 genomes]
rs7546409	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9633480	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005183	chr1:77728990-77949309	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv535010	chr1:77728990-77949309	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv932557	chr1:77730247-77958687	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1003714	chr1:77756861-77949309	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7512893	GIPC2	cis	cerebellum	SCAN
rs7512893	PIGK	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77872200-77893400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:77872200-77913800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:77872600-77884000	Weak transcription	HSMMtube	muscle
4	chr1:77876600-77888600	Strong transcription	HSMM	muscle
5	chr1:77877000-77883000	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr1:77877200-77880200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:77878000-77880200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr1:77878000-77887000	Weak transcription	Brain Angular Gyrus	brain
9	chr1:77878200-77881200	Strong transcription	NHDF-Ad	bronchial
10	chr1:77878400-77880200	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr1:77878400-77880200	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr1:77878400-77880200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:77878600-77880600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:77878600-77886400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:77878800-77880400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr1:77878800-77880600	Flanking Active TSS	GM12878-XiMat	blood
17	chr1:77878800-77881600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:77878800-77882000	Weak transcription	Osteobl	bone
19	chr1:77878800-77886400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:77879200-77880200	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr1:77879200-77881200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:77879200-77887200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:77879400-77880400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:77879400-77882400	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr1:77879400-77882800	Enhancers	Primary hematopoietic stem cells	blood
26	chr1:77879400-77883000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:77879600-77887200	Weak transcription	Fetal Thymus	thymus
28	chr1:77879600-77887800	Weak transcription	Brain Substantia Nigra	brain
29	chr1:77879800-77880800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:77879800-77882000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:77879800-77882000	Weak transcription	NHLF	lung
32	chr1:77879800-77882400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:77879800-77882600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:77879800-77883000	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr1:77879800-77883800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr1:77879800-77884600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr1:77879800-77885800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:77879800-77886600	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr1:77879800-77887200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:77879800-77887400	Weak transcription	Brain Hippocampus Middle	brain
41	chr1:77880000-77880200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
42	chr1:77880000-77880200	Enhancers	Primary T cells from cord blood	blood
43	chr1:77880000-77880400	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr1:77880000-77880800	Enhancers	Fetal Kidney	kidney
45	chr1:77880000-77882200	Bivalent Enhancer	Primary B cells from cord blood	blood
46	chr1:77880000-77883600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:77880000-77884800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr1:77880000-77887200	Weak transcription	Brain Anterior Caudate	brain

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