Variant report

Variant	rs786438
Chromosome Location	chr12:124091218-124091219
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:124084988..124092992-chr12:124114351..124121638,14	K562	blood:
2	chr12:124085831..124093816-chr12:124094373..124101211,18	MCF-7	breast:
3	chr12:124090616..124092389-chr12:124114546..124116542,2	MCF-7	breast:
4	chr12:124090038..124092401-chr12:124112202..124113711,2	K562	blood:
5	chr12:124090198..124092919-chr12:124093242..124095991,2	MCF-7	breast:
6	chr12:123848073..123850361-chr12:124091131..124093611,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139697	Chromatin interaction
ENSG00000111358	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000111364	Chromatin interaction
ENSG00000111361	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11057298	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11057302	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057306	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11610013	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615043	0.81[EUR][1000 genomes]
rs11834369	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837236	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12099981	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12099986	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877365	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2340691	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3209852	0.81[ASN][1000 genomes]
rs34099549	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930715	0.96[EUR][1000 genomes]
rs61678733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488881	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7136101	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7301377	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303554	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7316613	0.94[EUR][1000 genomes]
rs73414262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs786428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786433	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786437	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786450	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786455	0.80[EUR][1000 genomes]
rs7954782	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7958153	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960812	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7965466	0.84[EUR][1000 genomes]
rs7968040	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970545	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971779	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs952360	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers 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 miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv1042181	chr12:124037400-124152950	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs786438	DDX55	cis	Thyroid	GTEx
rs786438	DDX55	cis	lung	GTEx
rs786438	RP11-486O12.2	cis	Thyroid	GTEx
rs786438	RP11-486O12.2	cis	Esophagus Muscularis	GTEx
rs786438	RP11-486O12.2	cis	Nerve Tibial	GTEx
rs786438	RP11-486O12.2	cis	Adipose Subcutaneous	GTEx
rs786438	RP11-486O12.2	cis	Esophagus Mucosa	GTEx
rs786438	RP11-486O12.2	cis	Heart Left Ventricle	GTEx
rs786438	RP11-486O12.2	cis	Artery Aorta	GTEx
rs786438	DDX55	cis	Esophagus Muscularis	GTEx
rs786438	RP11-486O12.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124087600-124091800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:124087800-124091400	Weak transcription	Aorta	Aorta
3	chr12:124087800-124091400	Weak transcription	Brain Substantia Nigra	brain
4	chr12:124087800-124092000	Weak transcription	Small Intestine	intestine
5	chr12:124087800-124102000	Weak transcription	Stomach Mucosa	stomach
6	chr12:124087800-124109600	Weak transcription	Right Atrium	heart
7	chr12:124088000-124099200	Weak transcription	Fetal Heart	heart
8	chr12:124088000-124107200	Strong transcription	K562	blood
9	chr12:124088200-124098800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:124088200-124116000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:124088200-124117000	Strong transcription	Fetal Stomach	stomach
12	chr12:124088400-124091400	Weak transcription	Brain Angular Gyrus	brain
13	chr12:124088400-124096800	Strong transcription	Ovary	ovary
14	chr12:124088400-124097400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr12:124088400-124102400	Strong transcription	HUVEC	blood vessel
16	chr12:124088400-124103000	Strong transcription	Left Ventricle	heart
17	chr12:124088400-124105800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:124088400-124108000	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr12:124088400-124116000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:124088400-124116000	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr12:124088400-124116000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr12:124088400-124116000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:124088400-124116000	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr12:124088400-124116200	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr12:124088400-124116800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr12:124088400-124117000	Strong transcription	Fetal Intestine Small	intestine
27	chr12:124088600-124093200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr12:124088600-124096800	Strong transcription	Spleen	Spleen
29	chr12:124088600-124099200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:124088600-124103000	Strong transcription	Lung	lung
31	chr12:124088600-124104800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr12:124088600-124107400	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr12:124088600-124116000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:124088600-124116000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr12:124088600-124116000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr12:124088600-124116000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:124088600-124116000	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr12:124088600-124116000	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr12:124088600-124116200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr12:124088600-124116200	Strong transcription	Fetal Thymus	thymus
41	chr12:124088600-124116800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr12:124088600-124116800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr12:124088600-124116800	Strong transcription	Fetal Muscle Trunk	muscle
44	chr12:124088600-124117000	Strong transcription	Primary B cells from peripheral blood	blood
45	chr12:124088800-124098000	Strong transcription	A549	lung
46	chr12:124088800-124102800	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr12:124088800-124107600	Strong transcription	NH-A	brain
48	chr12:124088800-124116000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:124088800-124116000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr12:124088800-124116000	Strong transcription	Fetal Intestine Large	intestine

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