Variant report

Variant	rs9458259
Chromosome Location	chr6:161866482-161866483
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	chr6:161864849..161867369-chr6:162020785..162023410,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1886238	1.00[ASW][hapmap];1.00[AMR][1000 genomes]
rs1886239	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58063982	1.00[AMR][1000 genomes]
rs73600931	1.00[AMR][1000 genomes]
rs73600947	1.00[AMR][1000 genomes]
rs73600950	1.00[AMR][1000 genomes]
rs7758262	1.00[AMR][1000 genomes]
rs7758417	1.00[AMR][1000 genomes]
rs9456667	1.00[AMR][1000 genomes]
rs9456668	1.00[AMR][1000 genomes]
rs9456669	1.00[AMR][1000 genomes]
rs9456670	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv481931	chr6:161647026-161961906	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv1031234	chr6:161676768-162250726	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv886819	chr6:161712035-162520133	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv886820	chr6:161712880-162184932	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv830854	chr6:161739926-161927515	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv518931	chr6:161793319-162406335	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv481861	chr6:161802883-162160197	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv481981	chr6:161829077-162215745	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1033603	chr6:161844266-162001436	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv481750	chr6:161850976-161996586	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv481932	chr6:161862158-162097499	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9458259	HNMT	trans	lymphoblastoid	seeQTL
rs9458259	ARHGAP20	trans	lymphoblastoid	seeQTL
rs9458259	DAB2	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161860600-161871000	Weak transcription	Right Atrium	heart
2	chr6:161862600-161868600	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr6:161862800-161867600	Enhancers	Fetal Brain Male	brain
4	chr6:161863400-161867600	Enhancers	HSMM	muscle
5	chr6:161864400-161867600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:161864400-161867600	Enhancers	Fetal Muscle Leg	muscle
7	chr6:161864600-161866600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:161864600-161866800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:161864800-161866800	Enhancers	Fetal Brain Female	brain
10	chr6:161864800-161866800	Enhancers	Rectal Smooth Muscle	rectum
11	chr6:161864800-161866800	Enhancers	HSMMtube	muscle
12	chr6:161864800-161867000	Enhancers	Fetal Kidney	kidney
13	chr6:161864800-161867000	Enhancers	Pancreas	Pancrea
14	chr6:161864800-161867000	Enhancers	NH-A	brain
15	chr6:161865000-161866600	Enhancers	Brain Angular Gyrus	brain
16	chr6:161865000-161866600	Enhancers	Ovary	ovary
17	chr6:161865000-161867600	Enhancers	Adipose Nuclei	Adipose
18	chr6:161865000-161867600	Enhancers	Fetal Muscle Trunk	muscle
19	chr6:161865200-161866600	Enhancers	NHLF	lung
20	chr6:161865400-161866600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:161865400-161866600	Enhancers	Brain Substantia Nigra	brain
22	chr6:161865400-161866800	Enhancers	Fetal Lung	lung
23	chr6:161865400-161867800	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr6:161865800-161866600	Weak transcription	Lung	lung
25	chr6:161865800-161868200	Enhancers	Brain Germinal Matrix	brain
26	chr6:161866000-161866600	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr6:161866000-161867000	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr6:161866200-161866600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr6:161866200-161866600	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr6:161866200-161866600	Enhancers	Esophagus	oesophagus
31	chr6:161866200-161866600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr6:161866200-161866800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr6:161866200-161866800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr6:161866200-161867000	Bivalent Enhancer	Fetal Stomach	stomach
35	chr6:161866200-161867400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:161866200-161867400	Enhancers	Right Ventricle	heart
37	chr6:161866200-161867600	Enhancers	Psoas Muscle	Psoas
38	chr6:161866400-161866600	Enhancers	Brain Hippocampus Middle	brain
39	chr6:161866400-161866800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr6:161866400-161866800	Enhancers	Brain Anterior Caudate	brain
41	chr6:161866400-161866800	Enhancers	Brain Cingulate Gyrus	brain
42	chr6:161866400-161867200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:161866400-161867200	Weak transcription	Colon Smooth Muscle	Colon
44	chr6:161866400-161867400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:161866400-161867400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr6:161866400-161867400	Enhancers	Muscle Satellite Cultured Cells	--
47	chr6:161866400-161868800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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