Variant report

Variant	rs1934225
Chromosome Location	chr6:149416054-149416055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:149409974..149412815-chr6:149414835..149416934,2	K562	blood:
2	chr6:149411028..149414367-chr6:149415075..149417889,3	MCF-7	breast:
3	chr6:149381088..149383058-chr6:149414648..149416261,2	MCF-7	breast:
4	chr6:149350211..149352689-chr6:149414804..149416948,2	MCF-7	breast:
5	chr6:149414327..149416507-chr6:149637915..149640707,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000055208	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10872630	0.93[CHB][hapmap];0.86[ASN][1000 genomes]
rs10872631	0.93[CHB][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.86[ASN][1000 genomes]
rs11755147	0.81[CEU][hapmap];0.93[CHB][hapmap];0.94[GIH][hapmap];0.85[TSI][hapmap];0.85[ASN][1000 genomes]
rs11759315	0.82[CHB][hapmap]
rs12211152	0.80[CHB][hapmap];0.82[ASN][1000 genomes]
rs17669693	0.82[CHB][hapmap]
rs17732007	1.00[CHB][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.86[ASN][1000 genomes]
rs1934218	0.81[CHB][hapmap]
rs1934220	0.82[CHB][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap]
rs2879862	0.86[ASN][1000 genomes]
rs3935945	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs4073018	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4897077	0.84[ASN][1000 genomes]
rs4897078	0.93[CHB][hapmap];0.88[ASN][1000 genomes]
rs4897080	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62426156	0.86[ASN][1000 genomes]
rs6903827	0.93[CHB][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.88[ASN][1000 genomes]
rs6927215	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6932386	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs6939103	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs7772696	0.93[CHB][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032319	chr6:149271433-149550525	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv538470	chr6:149271433-149550525	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv830842	chr6:149272321-149427340	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv1024776	chr6:149398652-149654593	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1934225	PLEKHG1	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149402400-149416200	Weak transcription	Fetal Heart	heart
2	chr6:149410800-149418400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:149414200-149417600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr6:149414200-149418400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr6:149414400-149416200	Enhancers	Fetal Lung	lung
6	chr6:149414400-149416400	Enhancers	Muscle Satellite Cultured Cells	--
7	chr6:149414400-149416400	Enhancers	NH-A	brain
8	chr6:149414600-149416200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:149414600-149416400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:149414600-149416600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:149414600-149416600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr6:149414600-149416800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:149414600-149416800	Enhancers	Osteobl	bone
14	chr6:149414600-149417200	Enhancers	Fetal Stomach	stomach
15	chr6:149414600-149417400	Enhancers	Rectal Smooth Muscle	rectum
16	chr6:149414600-149417600	Enhancers	Primary T cells from cord blood	blood
17	chr6:149414800-149416200	Enhancers	Ovary	ovary
18	chr6:149414800-149416400	Enhancers	Placenta	Placenta
19	chr6:149414800-149418000	Enhancers	Primary hematopoietic stem cells	blood
20	chr6:149415000-149416200	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr6:149415000-149416200	Enhancers	Brain Substantia Nigra	brain
22	chr6:149415000-149416600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:149415000-149417400	Enhancers	Fetal Kidney	kidney
24	chr6:149415200-149416200	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr6:149415200-149416600	Enhancers	GM12878-XiMat	blood
26	chr6:149415200-149417200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:149415200-149418200	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr6:149415200-149419800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:149415400-149416200	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr6:149415400-149416400	Weak transcription	Adipose Nuclei	Adipose
31	chr6:149415400-149416400	Enhancers	Brain Anterior Caudate	brain
32	chr6:149415400-149418400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:149415600-149416600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr6:149415600-149416800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:149415600-149416800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:149415600-149416800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr6:149415600-149417000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr6:149415600-149417000	Weak transcription	Fetal Thymus	thymus
39	chr6:149415600-149418000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr6:149415800-149416400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr6:149415800-149417800	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr6:149416000-149416200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr6:149416000-149416200	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr6:149416000-149416400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
45	chr6:149416000-149416400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr6:149416000-149416400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr6:149416000-149416400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr6:149416000-149416400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr6:149416000-149416400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr6:149416000-149417000	Weak transcription	Placenta Amnion	Placenta Amnion

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