Variant report

Variant	rs1798563
Chromosome Location	chr12:123265952-123265953
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123236945..123239092-chr12:123263522..123266278,3	K562	blood:
2	chr12:123258957..123263504-chr12:123263837..123267205,4	MCF-7	breast:
3	chr12:123259286..123261214-chr12:123265092..123266921,2	K562	blood:

Variant related genes	Relation type
ENSG00000139726	Chromatin interaction
ENSG00000130783	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1026395	1.00[JPT][hapmap]
rs1037593	1.00[JPT][hapmap]
rs10773599	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs10847742	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs10847749	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs10847751	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs10847775	0.90[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs10847910	1.00[JPT][hapmap]
rs10848148	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11059729	1.00[ASN][1000 genomes]
rs11060152	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs11060932	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11060999	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12311043	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12369710	0.81[EUR][1000 genomes]
rs1260121	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12811036	0.84[EUR][1000 genomes]
rs12815479	1.00[CHD][hapmap]
rs1671684	1.00[JPT][hapmap]
rs1671687	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1696355	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1975761	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061099	1.00[JPT][hapmap]
rs2343107	1.00[JPT][hapmap]
rs2649894	0.87[ASN][1000 genomes]
rs2649895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649896	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649900	1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649914	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2656812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3844369	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs3852535	0.87[EUR][1000 genomes]
rs4038070	0.84[EUR][1000 genomes]
rs4038080	0.87[EUR][1000 genomes]
rs4038081	0.87[EUR][1000 genomes]
rs4307760	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs4424710	0.85[EUR][1000 genomes]
rs4426165	0.80[EUR][1000 genomes]
rs4759353	1.00[JPT][hapmap]
rs4759354	1.00[JPT][hapmap]
rs4759384	1.00[JPT][hapmap]
rs4759391	0.84[EUR][1000 genomes]
rs4759438	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs548349	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6489241	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs651683	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138257	1.00[JPT][hapmap]
rs7298176	1.00[JPT][hapmap]
rs7306948	1.00[JPT][hapmap]
rs7485652	1.00[JPT][hapmap]
rs7957643	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs7958155	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs839354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839355	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839356	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839357	1.00[ASN][1000 genomes]
rs839362	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs897386	0.81[CEU][hapmap]
rs897388	1.00[JPT][hapmap]
rs967281	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs9795629	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899571	chr12:123215734-123363562	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1798563	RAB35	cis	parietal	SCAN
rs1798563	KDM2B	cis	cerebellum	SCAN
rs1798563	TMEM120B	cis	parietal	SCAN
rs1798563	EIF2B1	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123259400-123266600	Weak transcription	Spleen	Spleen
2	chr12:123259400-123310600	Weak transcription	HSMMtube	muscle
3	chr12:123259800-123266200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:123259800-123285800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:123259800-123310600	Weak transcription	Brain Substantia Nigra	brain
6	chr12:123260000-123267200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr12:123260000-123267200	Weak transcription	Fetal Brain Male	brain
8	chr12:123260000-123268000	Weak transcription	Ovary	ovary
9	chr12:123260000-123268400	Weak transcription	Brain Anterior Caudate	brain
10	chr12:123260000-123272600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr12:123260000-123272800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:123260000-123275200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:123260000-123278400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:123260000-123278400	Weak transcription	Brain Angular Gyrus	brain
15	chr12:123260000-123278400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr12:123260000-123278400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr12:123260000-123303600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr12:123260200-123266200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr12:123260200-123266600	Weak transcription	Adipose Nuclei	Adipose
20	chr12:123260200-123268600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:123260200-123268600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:123260200-123270400	Weak transcription	Primary B cells from peripheral blood	blood
23	chr12:123260200-123272400	Weak transcription	HMEC	breast
24	chr12:123260200-123272400	Weak transcription	NHEK	skin
25	chr12:123260200-123272800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:123260200-123272800	Weak transcription	Left Ventricle	heart
27	chr12:123260200-123272800	Weak transcription	Osteobl	bone
28	chr12:123260200-123273000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:123260200-123273000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:123260200-123273000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:123260200-123273000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:123260200-123275400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:123260200-123278000	Weak transcription	Fetal Thymus	thymus
34	chr12:123260200-123284000	Weak transcription	Primary B cells from cord blood	blood
35	chr12:123260200-123284000	Weak transcription	Primary T cells from cord blood	blood
36	chr12:123260400-123270400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr12:123262600-123272800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:123263200-123275000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:123264200-123266600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:123264200-123268400	Weak transcription	Dnd41	blood
41	chr12:123264200-123272800	Weak transcription	HSMM	muscle
42	chr12:123264200-123278400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr12:123264200-123290800	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr12:123264600-123278400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:123265400-123266000	Strong transcription	Brain Hippocampus Middle	brain
46	chr12:123265600-123303600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr12:123265800-123275000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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