Variant report

Variant	rs9469598
Chromosome Location	chr6:33794167-33794168
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33792540..33794242-chr6:33797299..33799523,2	K562	blood:
2	chr6:33788574..33790183-chr6:33793587..33795973,2	MCF-7	breast:
3	chr6:33793637..33795279-chr6:33797318..33799112,2	MCF-7	breast:
4	chr6:33791904..33795612-chr6:33806607..33809462,3	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11754648	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535951	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535952	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3998111	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72657681	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9461910	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461912	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461913	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9461914	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9461915	0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9469595	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9469596	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9469597	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469600	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469601	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469602	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv885773	chr6:33778964-33813043	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv885774	chr6:33778964-33840121	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv885775	chr6:33788055-33828178	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9469598	LHFPL5	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33789400-33795000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:33790800-33796000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:33790800-33796000	Weak transcription	Right Ventricle	heart
4	chr6:33791000-33796000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:33791000-33796200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:33791000-33796400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr6:33791600-33796400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:33791800-33795400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr6:33792400-33794600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:33792600-33794200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:33792600-33795000	Weak transcription	Fetal Intestine Small	intestine
12	chr6:33792600-33795200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:33792600-33795800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr6:33792800-33794800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:33792800-33795000	Weak transcription	Fetal Intestine Large	intestine
16	chr6:33792800-33795800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:33792800-33797000	Weak transcription	Ovary	ovary
18	chr6:33793000-33794600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:33793000-33795000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr6:33793000-33795000	Weak transcription	Osteobl	bone
21	chr6:33793000-33795200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:33793000-33795200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:33793000-33795200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr6:33793000-33795400	Weak transcription	Colonic Mucosa	Colon
25	chr6:33793000-33795800	Weak transcription	Fetal Kidney	kidney
26	chr6:33793000-33795800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr6:33793000-33795800	Weak transcription	A549	lung
28	chr6:33793000-33796000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr6:33793000-33798800	Weak transcription	Spleen	Spleen
30	chr6:33793600-33794400	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr6:33794000-33794600	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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