Variant report

Variant	rs1405069
Chromosome Location	chr6:36922684-36922685
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:36922482..36924199-chr6:36953592..36955477,2	K562	blood:

Variant related genes	Relation type
ENSG00000137409	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1046279	0.81[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs1063021	0.93[EUR][1000 genomes]
rs1150786	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1405070	0.97[ASN][1000 genomes]
rs16889316	0.82[CHB][hapmap]
rs2296934	0.82[CHB][hapmap]
rs4714025	0.87[CHB][hapmap]
rs697746	0.87[ASN][1000 genomes]
rs707542	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs707998	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv519499	chr6:36915906-36924102	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv522653	chr6:36915906-36925774	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv885815	chr6:36915906-36979583	Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Chemerin levels	20237162	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1405069	SRPK1	cis	parietal	SCAN
rs1405069	PI16	cis	cerebellum	SCAN
rs1405069	CDKN1A	cis	cerebellum	SCAN
rs1405069	C6orf1	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36916000-36923000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:36916200-36923000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr6:36917600-36931200	Weak transcription	Brain Hippocampus Middle	brain
4	chr6:36918000-36923000	Weak transcription	Brain Substantia Nigra	brain
5	chr6:36918000-36924000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:36918200-36922800	Weak transcription	Hela-S3	cervix
7	chr6:36918200-36923000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:36918200-36923000	Weak transcription	NHEK	skin
9	chr6:36918200-36923200	Weak transcription	NH-A	brain
10	chr6:36918200-36927800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:36918200-36928400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr6:36921400-36922800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:36921400-36923200	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr6:36921400-36924000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:36921400-36924200	Enhancers	Primary hematopoietic stem cells	blood
16	chr6:36921400-36924400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:36921400-36924400	Enhancers	Thymus	Thymus
18	chr6:36921400-36925000	Enhancers	Fetal Thymus	thymus
19	chr6:36921600-36923200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr6:36921600-36924400	Enhancers	Fetal Heart	heart
21	chr6:36921600-36925000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr6:36921800-36923600	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr6:36921800-36923600	Enhancers	Dnd41	blood
24	chr6:36921800-36923800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
25	chr6:36921800-36923800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr6:36921800-36926200	Enhancers	Stomach Mucosa	stomach
27	chr6:36921800-36931200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr6:36922000-36923000	Weak transcription	Left Ventricle	heart
29	chr6:36922000-36924000	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr6:36922000-36924200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr6:36922000-36924200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr6:36922000-36931000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr6:36922200-36922800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
34	chr6:36922200-36923000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:36922200-36923000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
36	chr6:36922200-36923200	Weak transcription	GM12878-XiMat	blood
37	chr6:36922200-36924200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
38	chr6:36922200-36924600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
39	chr6:36922200-36929200	Weak transcription	Spleen	Spleen
40	chr6:36922400-36922800	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr6:36922400-36922800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr6:36922400-36922800	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr6:36922400-36923000	Active TSS	Brain Cingulate Gyrus	brain
44	chr6:36922400-36923200	Bivalent/Poised TSS	Adipose Nuclei	Adipose
45	chr6:36922400-36923800	Active TSS	Right Atrium	heart
46	chr6:36922400-36924200	Enhancers	Placenta	Placenta
47	chr6:36922600-36923000	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr6:36922600-36923200	Enhancers	Brain Anterior Caudate	brain
49	chr6:36922600-36923400	Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr6:36922600-36924000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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