Variant report

Variant	rs12082619
Chromosome Location	chr1:224416985-224416986
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	chr1:224395391..224399325-chr1:224414771..224417344,4	K562	blood:

Variant related genes	Relation type
ENSG00000232628	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10799491	0.80[EUR][1000 genomes]
rs10799507	0.88[EUR][1000 genomes]
rs10799543	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916458	0.92[EUR][1000 genomes]
rs10916462	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10916472	0.88[EUR][1000 genomes]
rs10916481	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916497	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916498	0.96[EUR][1000 genomes]
rs12083770	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120308	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124547	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126765	0.88[EUR][1000 genomes]
rs12126815	0.84[EUR][1000 genomes]
rs12133599	0.88[EUR][1000 genomes]
rs12138866	0.92[EUR][1000 genomes]
rs12140137	0.92[EUR][1000 genomes]
rs12184283	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45583539	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60256604	0.88[EUR][1000 genomes]
rs6660194	0.88[EUR][1000 genomes]
rs6686449	0.92[EUR][1000 genomes]
rs6701036	0.81[EUR][1000 genomes]
rs68073536	0.96[EUR][1000 genomes]
rs72753956	0.88[EUR][1000 genomes]
rs72753969	0.88[EUR][1000 genomes]
rs72753980	0.80[EUR][1000 genomes]
rs72753994	0.88[EUR][1000 genomes]
rs72754000	0.92[EUR][1000 genomes]
rs72754001	0.85[EUR][1000 genomes]
rs72755905	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7514140	0.88[EUR][1000 genomes]
rs7552239	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873223	chr1:224367232-224467117	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
2	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12082619	CNIH4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224401800-224427600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:224401800-224475400	Weak transcription	Esophagus	oesophagus
3	chr1:224407600-224434000	Weak transcription	Fetal Brain Male	brain
4	chr1:224411400-224417400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:224411600-224438000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:224411600-224454400	Weak transcription	Psoas Muscle	Psoas
7	chr1:224412000-224433000	Weak transcription	Fetal Heart	heart
8	chr1:224412200-224423200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:224412200-224423400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:224412200-224424800	Weak transcription	Stomach Mucosa	stomach
11	chr1:224412400-224473600	Weak transcription	HepG2	liver
12	chr1:224412600-224417400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:224413200-224432600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr1:224413600-224417400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:224413800-224419600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:224413800-224428000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:224413800-224428200	Strong transcription	Fetal Muscle Trunk	muscle
18	chr1:224414000-224432200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:224414200-224417800	Strong transcription	Colonic Mucosa	Colon
20	chr1:224414200-224417800	Strong transcription	Lung	lung
21	chr1:224414200-224418000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:224414200-224418000	Strong transcription	Brain Hippocampus Middle	brain
23	chr1:224414200-224418000	Strong transcription	Thymus	Thymus
24	chr1:224414200-224418200	Strong transcription	Fetal Muscle Leg	muscle
25	chr1:224414200-224419200	Strong transcription	Primary B cells from peripheral blood	blood
26	chr1:224414200-224421000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:224414200-224421000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:224414200-224421000	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr1:224414200-224421400	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:224414200-224422200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:224414200-224422600	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:224414200-224422600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr1:224414200-224424200	Strong transcription	Fetal Thymus	thymus
34	chr1:224414200-224425000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:224414200-224425000	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr1:224414200-224426200	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr1:224414200-224427800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:224414200-224427800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr1:224414200-224428800	Strong transcription	Fetal Intestine Large	intestine
40	chr1:224414200-224438000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:224414400-224417000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:224414400-224417800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:224414400-224418400	Strong transcription	HSMMtube	muscle
44	chr1:224414400-224419600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr1:224414400-224419600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:224414400-224423000	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr1:224414400-224424400	Strong transcription	Placenta	Placenta
48	chr1:224414400-224428800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:224414600-224418000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr1:224414600-224418000	Strong transcription	Stomach Smooth Muscle	stomach

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