Variant report

Variant	rs1976919
Chromosome Location	chr3:119215299-119215300
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119201366..119207142-chr3:119210949..119217240,7	K562	blood:
2	chr3:119185641..119191138-chr3:119214841..119219392,9	MCF-7	breast:
3	chr3:119181870..119185760-chr3:119214240..119218868,7	K562	blood:
4	chr3:119186169..119189555-chr3:119214375..119219589,12	K562	blood:
5	chr3:119185037..119191105-chr3:119214944..119221331,23	MCF-7	breast:
6	chr3:119213354..119215944-chr3:119217357..119219322,2	K562	blood:

Variant related genes	Relation type
ENSG00000176142	Chromatin interaction
ENSG00000113845	Chromatin interaction
ENSG00000163389	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1060569	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13080905	0.94[ASN][1000 genomes]
rs1797839	0.91[ASN][1000 genomes]
rs1900742	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1919586	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1919590	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1967621	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2030816	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2177812	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732413	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3814397	0.91[ASN][1000 genomes]
rs4687855	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4687860	0.94[ASN][1000 genomes]
rs4688005	0.96[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4688007	0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4688008	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688012	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688014	0.89[ASN][1000 genomes]
rs6414282	0.91[ASN][1000 genomes]
rs6414283	0.96[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6438528	0.94[ASN][1000 genomes]
rs6438529	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6438530	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6438531	0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6438535	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6777535	0.94[ASN][1000 genomes]
rs6778945	0.92[ASN][1000 genomes]
rs6794822	0.91[ASN][1000 genomes]
rs6796970	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs727905	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7430798	0.94[ASN][1000 genomes]
rs7621259	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628626	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7630587	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7642502	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289129	0.94[ASN][1000 genomes]
rs9809155	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9836326	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9836627	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850447	0.92[ASN][1000 genomes]
rs9867768	0.92[ASN][1000 genomes]
rs9873196	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874480	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9877854	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic 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	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1976919	UPK1B	cis	brain	BrainEAC

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119188400-119216200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:119188400-119216800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:119188600-119216200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:119188800-119216200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:119189000-119216200	Weak transcription	Stomach Mucosa	stomach
6	chr3:119189000-119216200	Weak transcription	HUVEC	blood vessel
7	chr3:119189000-119216600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:119189800-119216000	Weak transcription	Fetal Heart	heart
9	chr3:119190800-119216400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:119191000-119216400	Weak transcription	Fetal Brain Male	brain
11	chr3:119192400-119216400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:119196400-119216200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:119196400-119216600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:119196800-119216800	Weak transcription	Small Intestine	intestine
15	chr3:119197000-119216400	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:119197400-119216600	Weak transcription	Aorta	Aorta
17	chr3:119204800-119216400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:119205000-119216000	Weak transcription	Fetal Kidney	kidney
19	chr3:119205400-119216400	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr3:119205600-119216600	Weak transcription	Colonic Mucosa	Colon
21	chr3:119205600-119216600	Weak transcription	Esophagus	oesophagus
22	chr3:119205600-119216600	Weak transcription	Gastric	stomach
23	chr3:119205800-119216000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:119205800-119216200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:119205800-119216200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:119205800-119216200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:119205800-119216600	Weak transcription	Pancreas	Pancrea
28	chr3:119205800-119217000	Weak transcription	Spleen	Spleen
29	chr3:119206000-119216200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:119206000-119216200	Weak transcription	Fetal Lung	lung
31	chr3:119206000-119216200	Weak transcription	Psoas Muscle	Psoas
32	chr3:119206000-119216600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr3:119206200-119216000	Weak transcription	NHLF	lung
34	chr3:119206200-119216200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr3:119206200-119216200	Weak transcription	NH-A	brain
36	chr3:119206400-119216200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr3:119206800-119216200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr3:119206800-119216200	Weak transcription	Brain Anterior Caudate	brain
39	chr3:119207000-119216800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr3:119207200-119215800	Weak transcription	HepG2	liver
41	chr3:119207200-119216200	Weak transcription	Hela-S3	cervix
42	chr3:119207200-119216600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:119207400-119216600	Weak transcription	Ovary	ovary
44	chr3:119207600-119216200	Weak transcription	HSMMtube	muscle
45	chr3:119207600-119216400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr3:119207800-119216600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr3:119208200-119216200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr3:119208600-119216600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:119208800-119216200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:119208800-119216200	Weak transcription	Fetal Intestine Small	intestine

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