Variant report

Variant	rs1962039
Chromosome Location	chr7:129351720-129351721
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:129349986..129354083-chr7:129418762..129421039,4	MCF-7	breast:
2	chr7:129350668..129352868-chr7:129358441..129360338,2	K562	blood:
3	chr7:129350525..129352273-chr7:129405783..129407526,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10243809	0.94[AFR][1000 genomes]
rs1882094	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[ASN][1000 genomes]
rs3778775	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4272311	0.86[ASN][1000 genomes]
rs4731617	0.84[ASW][hapmap];0.98[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs4731621	0.80[YRI][hapmap]
rs62489295	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6467259	0.86[YRI][hapmap]
rs6946418	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[ASN][1000 genomes]
rs6969441	0.85[CHB][hapmap]
rs7778681	0.89[ASN][1000 genomes]
rs7782520	0.86[ASN][1000 genomes]
rs7807898	0.86[YRI][hapmap]
rs9641854	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9641855	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs9656383	0.94[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1962039	COPG2	cis	parietal	SCAN
rs1962039	TNPO3	cis	parietal	SCAN
rs1962039	TNPO3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:129307200-129352000	Weak transcription	NHLF	lung
2	chr7:129311400-129352200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:129315400-129357000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr7:129315600-129373600	Weak transcription	Psoas Muscle	Psoas
5	chr7:129316400-129357200	Weak transcription	Fetal Brain Male	brain
6	chr7:129319000-129380000	Weak transcription	NHDF-Ad	bronchial
7	chr7:129328000-129369000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr7:129332400-129351800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr7:129332800-129352200	Weak transcription	Right Ventricle	heart
10	chr7:129337600-129359200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr7:129339200-129356800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr7:129339200-129381800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr7:129342800-129360200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr7:129342800-129367000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr7:129343200-129379600	Weak transcription	Stomach Mucosa	stomach
16	chr7:129343400-129361200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr7:129345200-129355800	Strong transcription	Thymus	Thymus
18	chr7:129345600-129355200	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr7:129345800-129355000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr7:129345800-129359200	Strong transcription	Fetal Thymus	thymus
21	chr7:129346800-129372400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:129347000-129360200	Strong transcription	Primary B cells from peripheral blood	blood
23	chr7:129348000-129352800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr7:129348200-129355600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr7:129348200-129375600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr7:129348200-129392000	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr7:129348400-129352200	Weak transcription	Fetal Heart	heart
28	chr7:129348400-129354800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr7:129348400-129372400	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr7:129348400-129372400	Strong transcription	Dnd41	blood
31	chr7:129348600-129352800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr7:129348600-129355200	Strong transcription	Adipose Nuclei	Adipose
33	chr7:129348600-129355200	Strong transcription	GM12878-XiMat	blood
34	chr7:129348600-129355400	Strong transcription	Primary hematopoietic stem cells	blood
35	chr7:129348600-129355400	Strong transcription	Liver	Liver
36	chr7:129348600-129355600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr7:129348600-129355600	Strong transcription	Placenta	Placenta
38	chr7:129348600-129355800	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr7:129348600-129360600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr7:129348600-129360600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr7:129348600-129360600	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr7:129348600-129360800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr7:129348600-129361200	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr7:129348600-129372400	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr7:129348600-129372600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr7:129348600-129375200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr7:129348600-129375800	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr7:129348800-129352400	Strong transcription	Left Ventricle	heart
49	chr7:129348800-129353000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr7:129348800-129355000	Strong transcription	Spleen	Spleen

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