Variant report

Variant	rs9296095
Chromosome Location	chr6:33542523-33542524
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:33541749..33544429-chr6:33546198..33547784,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10807126	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10947409	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11968218	0.90[ASN][1000 genomes]
rs12206050	0.94[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.83[ASN][1000 genomes]
rs12213869	0.87[GIH][hapmap]
rs12214883	0.88[ASN][1000 genomes]
rs210157	0.81[ASN][1000 genomes]
rs3748079	0.84[GIH][hapmap];0.80[MEX][hapmap]
rs3846855	0.94[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs510153	0.87[GIH][hapmap]
rs5745568	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5745582	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745587	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61292931	0.93[AFR][1000 genomes]
rs6914422	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6925471	0.88[AFR][1000 genomes]
rs9357161	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9366824	0.90[ASN][1000 genomes]
rs9380365	0.88[CHB][hapmap]
rs9380371	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9469485	1.00[CHB][hapmap];0.95[YRI][hapmap];0.80[AMR][1000 genomes];0.87[ASN][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	nsv462896	chr6:33534880-33588147	Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv602833	chr6:33534880-33588147	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv519079	chr6:33540209-33542538	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Platelet counts	25705162	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9296095	LHFPL5	cis	parietal	SCAN
rs9296095	BAK1	cis	multi-tissue	Pritchard
rs9296095	BAK1	cis	Whole Blood	GTEx
rs9296095	CDKN1A	cis	parietal	SCAN
rs9296095	PIM1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33539200-33547200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:33539600-33542800	Weak transcription	A549	lung
3	chr6:33539600-33546200	Weak transcription	NHDF-Ad	bronchial
4	chr6:33539600-33546400	Weak transcription	Fetal Brain Male	brain
5	chr6:33539600-33547000	Weak transcription	Fetal Kidney	kidney
6	chr6:33539800-33544400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:33539800-33544400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr6:33539800-33545400	Strong transcription	Fetal Intestine Small	intestine
9	chr6:33539800-33546400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:33539800-33547000	Weak transcription	Psoas Muscle	Psoas
11	chr6:33540000-33543800	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr6:33540000-33544200	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr6:33540000-33545000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:33540000-33545000	Weak transcription	Right Atrium	heart
15	chr6:33540000-33546400	Strong transcription	Fetal Stomach	stomach
16	chr6:33540200-33543200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:33540200-33543600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:33540200-33544800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr6:33540200-33545000	Strong transcription	Lung	lung
20	chr6:33540200-33545800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:33540200-33545800	Strong transcription	Fetal Muscle Leg	muscle
22	chr6:33540200-33546000	Weak transcription	Fetal Heart	heart
23	chr6:33540400-33544400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:33540400-33544400	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr6:33540400-33544600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:33540400-33544600	Strong transcription	Fetal Thymus	thymus
27	chr6:33540400-33544800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:33540600-33543800	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr6:33540800-33544600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr6:33540800-33544600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr6:33540800-33544600	Strong transcription	Adipose Nuclei	Adipose
32	chr6:33541000-33543800	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr6:33541000-33544600	Strong transcription	Colonic Mucosa	Colon
34	chr6:33541000-33544800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:33541000-33545200	Strong transcription	Fetal Muscle Trunk	muscle
36	chr6:33541000-33545400	Strong transcription	Brain Germinal Matrix	brain
37	chr6:33541200-33544000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:33541200-33544400	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr6:33541200-33544400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr6:33541200-33544600	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr6:33541200-33544600	Strong transcription	Spleen	Spleen
42	chr6:33541200-33544800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr6:33541200-33545000	Strong transcription	Stomach Smooth Muscle	stomach
44	chr6:33541200-33545000	Strong transcription	Dnd41	blood
45	chr6:33541200-33545800	Strong transcription	Fetal Brain Female	brain
46	chr6:33541200-33546000	Strong transcription	Osteobl	bone
47	chr6:33541200-33546400	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr6:33541400-33543000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr6:33541400-33543800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:33541400-33544000	Strong transcription	Brain Substantia Nigra	brain

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