Variant report

Variant	rs3850825
Chromosome Location	chr1:247460727-247460728
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	chr1:247459842..247461547-chr1:247511493..247513856,2	K562	blood:
2	chr1:247459823..247461547-chr1:247511493..247514413,3	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10754545	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1192833	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.99[ASN][1000 genomes]
rs12023326	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12023478	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12026978	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12027522	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12034916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12034919	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12035371	0.92[ASN][1000 genomes]
rs12035515	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12047860	0.82[ASN][1000 genomes]
rs12048553	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12404914	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17664745	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56013900	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56322048	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56335231	0.88[ASN][1000 genomes]
rs56366903	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs56396334	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58522562	0.87[ASN][1000 genomes]
rs6426239	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.93[ASN][1000 genomes]
rs6690864	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.92[ASN][1000 genomes]
rs6697861	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7522071	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
3	esv3411043	chr1:247382851-247517729	Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
4	esv3378684	chr1:247382994-247518438	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
5	nsv833137	chr1:247437317-247607428	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3850825	NLRP3	cis	cerebellum	SCAN
rs3850825	ZNF496	cis	cerebellum	SCAN
rs3850825	ZNF496	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247449200-247462000	Weak transcription	Primary T cells from cord blood	blood
2	chr1:247449400-247460800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:247449600-247462400	Weak transcription	Brain Angular Gyrus	brain
4	chr1:247451000-247460800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:247452400-247460800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:247452600-247460800	Weak transcription	Brain Germinal Matrix	brain
7	chr1:247452600-247461200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:247452800-247462000	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:247453000-247460800	Weak transcription	Fetal Brain Female	brain
10	chr1:247453000-247462000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:247453400-247462000	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:247453400-247463000	Weak transcription	Brain Substantia Nigra	brain
13	chr1:247454200-247462600	Weak transcription	Pancreas	Pancrea
14	chr1:247454400-247461800	Enhancers	Fetal Thymus	thymus
15	chr1:247455000-247470400	Weak transcription	Fetal Brain Male	brain
16	chr1:247455200-247461000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:247455200-247463000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr1:247455400-247461200	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr1:247455600-247462600	Enhancers	H9 Cell Line	embryonic stem cell
20	chr1:247455800-247460800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:247455800-247462200	Enhancers	H1 Cell Line	embryonic stem cell
22	chr1:247455800-247462600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:247455800-247464200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:247456000-247462000	Weak transcription	Lung	lung
25	chr1:247456000-247493400	Weak transcription	Right Atrium	heart
26	chr1:247456200-247460800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr1:247456200-247462200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:247456600-247471400	Weak transcription	Fetal Heart	heart
29	chr1:247456800-247462000	Weak transcription	Ovary	ovary
30	chr1:247456800-247462200	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr1:247456800-247462400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr1:247457000-247465000	Weak transcription	Hela-S3	cervix
33	chr1:247457800-247463200	Weak transcription	Placenta	Placenta
34	chr1:247457800-247466000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:247458000-247461600	Weak transcription	Aorta	Aorta
36	chr1:247458000-247466800	Weak transcription	HSMMtube	muscle
37	chr1:247458200-247462000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:247458200-247462200	Weak transcription	HSMM	muscle
39	chr1:247458200-247462400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:247458200-247463000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr1:247458600-247461000	Weak transcription	Right Ventricle	heart
42	chr1:247458800-247462000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:247459000-247460800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:247459000-247461000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:247459000-247461600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:247459000-247462200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:247459000-247462200	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr1:247459000-247462400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:247459000-247462400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:247459000-247463600	Weak transcription	NH-A	brain

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