Variant report

Variant	rs140125
Chromosome Location	chr22:30146507-30146508
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30130941..30133818-chr22:30144985..30147499,2	MCF-7	breast:
2	chr22:30144553..30146905-chr22:30152166..30154338,3	MCF-7	breast:
3	chr22:30145045..30147687-chr22:30166151..30168873,2	MCF-7	breast:
4	chr22:30142692..30145269-chr22:30145289..30147345,2	K562	blood:
5	chr22:30144477..30147071-chr22:30161090..30163905,2	K562	blood:

Variant related genes	Relation type
ENSG00000184076	Chromatin interaction
ENSG00000100319	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1076137	0.84[EUR][1000 genomes]
rs131278	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs131291	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs131294	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs131296	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs140105	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs140108	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs140135	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs140142	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs140151	0.89[EUR][1000 genomes]
rs2349225	0.89[EUR][1000 genomes]
rs249400	0.86[EUR][1000 genomes]
rs36578	0.87[EUR][1000 genomes]
rs4820820	0.81[EUR][1000 genomes]
rs5752968	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv914964	chr22:30081715-30150549	Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv515720	chr22:30081715-30163526	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1065072	chr22:30102176-30155245	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs140125	UCRC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30123600-30146800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:30123600-30147000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr22:30130200-30150200	Weak transcription	A549	lung
4	chr22:30130400-30150600	Strong transcription	Fetal Intestine Small	intestine
5	chr22:30130600-30149800	Weak transcription	Psoas Muscle	Psoas
6	chr22:30131400-30148600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr22:30131600-30162000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr22:30131800-30147200	Strong transcription	Brain Inferior Temporal Lobe	brain
9	chr22:30134400-30158400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr22:30136000-30154800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr22:30136600-30146600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr22:30136600-30146600	Weak transcription	Fetal Heart	heart
13	chr22:30136600-30146800	Weak transcription	Small Intestine	intestine
14	chr22:30136800-30146600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr22:30139600-30147000	Strong transcription	Stomach Smooth Muscle	stomach
16	chr22:30139800-30146600	Strong transcription	Lung	lung
17	chr22:30141200-30150800	Strong transcription	Fetal Brain Female	brain
18	chr22:30141400-30146600	Strong transcription	Brain Germinal Matrix	brain
19	chr22:30141600-30154200	Weak transcription	Osteobl	bone
20	chr22:30141800-30146600	Strong transcription	Right Ventricle	heart
21	chr22:30141800-30147000	Strong transcription	Fetal Muscle Leg	muscle
22	chr22:30141800-30147000	Weak transcription	HMEC	breast
23	chr22:30141800-30147200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr22:30141800-30155400	Strong transcription	Fetal Stomach	stomach
25	chr22:30142000-30147000	Weak transcription	HepG2	liver
26	chr22:30142000-30150000	Strong transcription	Fetal Muscle Trunk	muscle
27	chr22:30142600-30147400	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr22:30142800-30146800	Strong transcription	Rectal Smooth Muscle	rectum
29	chr22:30143600-30147200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr22:30143600-30154200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr22:30143800-30147000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr22:30144000-30147800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr22:30144200-30146800	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr22:30144200-30146800	Enhancers	Esophagus	oesophagus
35	chr22:30144400-30146600	Weak transcription	Fetal Thymus	thymus
36	chr22:30144400-30148400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr22:30144400-30150000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr22:30144400-30150000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr22:30144400-30161800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr22:30144400-30162000	Weak transcription	Placenta	Placenta
41	chr22:30144400-30162200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr22:30144600-30146600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr22:30144600-30146600	Weak transcription	K562	blood
44	chr22:30144600-30146800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr22:30144600-30146800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr22:30144600-30147000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr22:30144600-30147000	Weak transcription	Liver	Liver
48	chr22:30144600-30148000	Weak transcription	Spleen	Spleen
49	chr22:30144600-30148600	Weak transcription	Fetal Intestine Large	intestine
50	chr22:30144600-30149800	Weak transcription	Thymus	Thymus

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