Variant report

Variant	rs12023326
Chromosome Location	chr1:247471121-247471122
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:247370419..247372444-chr1:247470264..247472870,2	K562	blood:
2	chr1:247467380..247471480-chr1:247472464..247476921,4	K562	blood:
3	chr1:247461556..247465350-chr1:247467126..247471967,7	K562	blood:
4	chr1:247469630..247471480-chr1:247475421..247477834,2	K562	blood:

Variant related genes	Relation type
ENSG00000162714	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10754545	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1192833	0.82[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12023478	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12026978	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12027522	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12034916	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12034919	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12035371	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12035515	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12047860	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12048553	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12404914	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17664745	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1771925	0.80[CEU][hapmap]
rs3850825	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]
rs56013900	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56322048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56335231	0.88[ASN][1000 genomes]
rs56366903	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56396334	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56740645	0.84[AMR][1000 genomes]
rs58522562	0.85[ASN][1000 genomes]
rs6426239	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6690864	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6697861	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7522071	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.99[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
rs12023326	ZNF496	Cis_1M	lymphoblastoid	RTeQTL
rs12023326	NLRP3	cis	cerebellum	SCAN
rs12023326	ZNF496	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247456000-247493400	Weak transcription	Right Atrium	heart
2	chr1:247456600-247471400	Weak transcription	Fetal Heart	heart
3	chr1:247459800-247485800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:247460400-247493400	Strong transcription	Fetal Muscle Leg	muscle
5	chr1:247460800-247471600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:247460800-247474200	Strong transcription	Brain Germinal Matrix	brain
7	chr1:247460800-247474800	Strong transcription	Brain Cingulate Gyrus	brain
8	chr1:247460800-247476200	Weak transcription	HMEC	breast
9	chr1:247460800-247479800	Strong transcription	Fetal Brain Female	brain
10	chr1:247460800-247481000	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr1:247460800-247491800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:247460800-247493400	Strong transcription	Fetal Muscle Trunk	muscle
13	chr1:247461000-247475400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:247461000-247485400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:247461200-247473600	Weak transcription	HUVEC	blood vessel
16	chr1:247461200-247485400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:247461200-247488200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:247461400-247471600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr1:247461400-247485400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:247461400-247493800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr1:247461600-247475200	Strong transcription	Aorta	Aorta
22	chr1:247461600-247481000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:247461800-247474200	Strong transcription	Stomach Smooth Muscle	stomach
24	chr1:247462000-247473800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:247462000-247473800	Strong transcription	Primary T cells from cord blood	blood
26	chr1:247462000-247474000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:247462000-247474000	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr1:247462200-247473800	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:247462200-247473800	Strong transcription	K562	blood
30	chr1:247462200-247480000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:247462400-247473800	Strong transcription	Duodenum Mucosa	Duodenum
32	chr1:247462400-247474000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:247462400-247474400	Strong transcription	Dnd41	blood
34	chr1:247462400-247475600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:247462600-247474000	Strong transcription	Fetal Intestine Small	intestine
36	chr1:247462600-247479200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:247462800-247473400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:247462800-247488000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:247463000-247473400	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr1:247463000-247474000	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr1:247463000-247475000	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr1:247463000-247477000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:247463000-247486200	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:247463000-247486400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:247463000-247493600	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:247463200-247473400	Strong transcription	Placenta	Placenta
47	chr1:247463200-247473800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:247463200-247481000	Strong transcription	Left Ventricle	heart
49	chr1:247463200-247493400	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr1:247463400-247473800	Strong transcription	H1 Cell Line	embryonic stem cell

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