Variant report

Variant	rs9355574
Chromosome Location	chr6:166774689-166774690
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:166751664..166755250-chr6:166772904..166776274,3	K562	blood:
2	chr6:166771550..166776527-chr6:166791729..166798170,6	K562	blood:

Variant related genes	Relation type
ENSG00000060762	Chromatin interaction
ENSG00000261420	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1546853	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1546854	1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1546855	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1569459	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1569460	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1569461	0.96[EUR][1000 genomes]
rs1977049	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1977050	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1977051	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1977052	0.91[EUR][1000 genomes]
rs1977053	0.90[EUR][1000 genomes]
rs1977054	0.90[EUR][1000 genomes]
rs1977056	0.89[EUR][1000 genomes]
rs1997661	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2179177	0.85[EUR][1000 genomes]
rs2343591	0.91[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs3734605	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3757194	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3757195	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4305699	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4709112	0.81[ASN][1000 genomes]
rs4710043	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6456078	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6456079	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6456081	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6902813	0.95[ASN][1000 genomes]
rs6905635	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6906844	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6909951	0.81[ASN][1000 genomes]
rs6912695	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6918091	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918135	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs735297	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7449594	0.83[EUR][1000 genomes]
rs7449629	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7744743	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7752716	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9283865	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9295338	0.90[EUR][1000 genomes]
rs9295341	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9295342	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9295343	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9295344	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9295345	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9348123	0.95[CEU][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9348124	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9348125	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9348126	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9355575	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9356482	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9356483	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9364845	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9364846	0.88[EUR][1000 genomes]
rs9364847	0.87[EUR][1000 genomes]
rs9364848	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9366009	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9366010	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	esv1797072	chr6:166766142-166782143	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9355574	BRP44L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166757000-166779200	Weak transcription	Right Atrium	heart
2	chr6:166765600-166776400	Weak transcription	Brain Hippocampus Middle	brain
3	chr6:166765600-166777000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:166765800-166776200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr6:166765800-166776200	Weak transcription	Brain Substantia Nigra	brain
6	chr6:166765800-166776600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:166765800-166778000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr6:166766800-166776400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:166769400-166775600	Weak transcription	Pancreas	Pancrea
10	chr6:166769400-166776600	Weak transcription	Gastric	stomach
11	chr6:166769400-166777800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr6:166770200-166776200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr6:166771000-166776600	Weak transcription	GM12878-XiMat	blood
14	chr6:166771400-166776600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr6:166771600-166776400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:166772000-166776200	Weak transcription	Thymus	Thymus
17	chr6:166772000-166776400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:166772000-166776400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:166772400-166775600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr6:166772600-166775600	Weak transcription	Fetal Stomach	stomach
21	chr6:166772800-166776200	Weak transcription	Fetal Lung	lung
22	chr6:166772800-166776400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr6:166773000-166776000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr6:166773000-166776400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr6:166773000-166776400	Weak transcription	Right Ventricle	heart
26	chr6:166773200-166776200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:166773200-166776200	Weak transcription	Fetal Intestine Small	intestine
28	chr6:166773200-166776400	Weak transcription	Brain Angular Gyrus	brain
29	chr6:166773200-166776400	Weak transcription	Brain Germinal Matrix	brain
30	chr6:166773200-166776400	Weak transcription	Fetal Intestine Large	intestine
31	chr6:166773200-166794600	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr6:166773400-166775200	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr6:166773400-166776600	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr6:166773400-166776600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr6:166773400-166790000	Weak transcription	Fetal Brain Male	brain
36	chr6:166773600-166776800	Weak transcription	Dnd41	blood
37	chr6:166773800-166774800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr6:166773800-166774800	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr6:166773800-166774800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:166773800-166774800	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr6:166773800-166775000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:166773800-166775000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr6:166773800-166775000	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr6:166773800-166775000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:166773800-166775000	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr6:166773800-166775000	Enhancers	HSMM	muscle
47	chr6:166773800-166775000	Enhancers	NHDF-Ad	bronchial
48	chr6:166773800-166775000	Enhancers	Osteobl	bone
49	chr6:166773800-166775800	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr6:166773800-166776000	Enhancers	Skeletal Muscle Male	skeletal muscle

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