Variant report

Variant	rs2349225
Chromosome Location	chr22:30193548-30193549
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:30186308..30188642-chr22:30191729..30194768,3	K562	blood:
2	chr22:30185624..30189974-chr22:30192313..30194980,5	MCF-7	breast:
3	chr22:30191639..30194644-chr22:30194985..30199113,4	K562	blood:
4	chr22:30191545..30194644-chr22:30195667..30197802,3	K562	blood:
5	chr22:30192738..30197507-chr22:30207918..30212414,7	MCF-7	breast:
6	chr22:30167944..30169824-chr22:30191784..30194571,2	MCF-7	breast:
7	chr22:30189139..30191071-chr22:30192199..30195286,3	K562	blood:
8	chr22:30193309..30197041-chr22:30202385..30207780,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000100325	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1071888	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1076137	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12168552	0.84[AMR][1000 genomes]
rs131278	0.95[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs131291	0.83[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs131294	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs131296	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs140105	0.91[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes]
rs140108	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[EUR][1000 genomes]
rs140125	0.89[EUR][1000 genomes]
rs140135	0.96[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs140142	0.92[EUR][1000 genomes]
rs140151	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17643918	0.84[AMR][1000 genomes]
rs2105870	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2412960	0.91[CEU][hapmap]
rs2412963	0.91[CEU][hapmap];0.89[JPT][hapmap]
rs249400	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34862234	0.84[AMR][1000 genomes]
rs35705048	0.84[AMR][1000 genomes]
rs36578	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36600	0.91[CEU][hapmap];0.88[JPT][hapmap]
rs36604	0.91[CEU][hapmap];0.88[JPT][hapmap]
rs3788423	0.91[CEU][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap]
rs3887275	0.91[CEU][hapmap];0.89[JPT][hapmap];0.80[YRI][hapmap]
rs3958025	0.91[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs4239932	0.91[CEU][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap]
rs4820820	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4820822	0.81[AMR][1000 genomes]
rs4823055	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4823063	0.91[CEU][hapmap];0.89[JPT][hapmap];0.80[YRI][hapmap]
rs4993442	0.85[AMR][1000 genomes]
rs5752968	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7286070	0.82[AMR][1000 genomes]
rs7292615	0.84[AMR][1000 genomes]
rs737909	0.91[CEU][hapmap];0.88[JPT][hapmap]
rs8139994	0.83[AMR][1000 genomes]
rs8141680	0.80[YRI][hapmap]
rs9620926	0.84[AMR][1000 genomes]
rs9625873	0.80[AMR][1000 genomes]
rs9625874	0.82[AMR][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	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv1829662	chr22:30171725-30304390	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	esv1829425	chr22:30184378-30297376	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2349225	UCRC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30166800-30194400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr22:30175400-30194000	Weak transcription	Hela-S3	cervix
3	chr22:30177600-30233000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr22:30181200-30196200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr22:30181200-30196200	Weak transcription	Fetal Heart	heart
6	chr22:30182000-30194600	Strong transcription	Sigmoid Colon	Sigmoid Colon
7	chr22:30182200-30194000	Strong transcription	Fetal Muscle Leg	muscle
8	chr22:30182200-30217000	Strong transcription	Fetal Intestine Small	intestine
9	chr22:30182200-30222200	Strong transcription	Thymus	Thymus
10	chr22:30182600-30194800	Strong transcription	Fetal Muscle Trunk	muscle
11	chr22:30182800-30194400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr22:30182800-30194600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr22:30182800-30194600	Strong transcription	Stomach Smooth Muscle	stomach
14	chr22:30182800-30204600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr22:30182800-30204800	Strong transcription	Fetal Brain Female	brain
16	chr22:30182800-30232200	Strong transcription	Primary T cells from cord blood	blood
17	chr22:30182800-30232200	Strong transcription	Fetal Stomach	stomach
18	chr22:30183000-30194000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr22:30183000-30194200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr22:30183000-30194200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr22:30183000-30194200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr22:30183000-30194400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr22:30183000-30194400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr22:30183000-30194400	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr22:30183000-30221400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr22:30183200-30194600	Strong transcription	Brain Inferior Temporal Lobe	brain
27	chr22:30183200-30197000	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr22:30183200-30230800	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr22:30183400-30194200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr22:30183400-30194200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr22:30183400-30194200	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr22:30183400-30204800	Strong transcription	Brain Germinal Matrix	brain
33	chr22:30183400-30224000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr22:30183400-30230800	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr22:30183600-30194000	Strong transcription	Left Ventricle	heart
36	chr22:30183600-30194400	Strong transcription	Dnd41	blood
37	chr22:30183600-30194600	Strong transcription	Brain Cingulate Gyrus	brain
38	chr22:30183800-30194200	Strong transcription	Brain Anterior Caudate	brain
39	chr22:30183800-30194400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr22:30183800-30194400	Strong transcription	Brain Angular Gyrus	brain
41	chr22:30183800-30204800	Strong transcription	Ovary	ovary
42	chr22:30183800-30205000	Strong transcription	Fetal Intestine Large	intestine
43	chr22:30183800-30205200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr22:30183800-30224000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr22:30183800-30232200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr22:30184000-30194600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr22:30184000-30198400	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr22:30184000-30204800	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr22:30184000-30222200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr22:30184200-30194400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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