Variant report

Variant	rs4930725
Chromosome Location	chr12:124428162-124428163
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr12:124427816-124428171	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:124427289..124429927-chr12:124454570..124456176,2	K562	blood:
2	chr12:124426014..124428363-chr12:124429735..124431659,2	K562	blood:
3	chr12:124426853..124428789-chr12:124454676..124457058,3	K562	blood:

Variant related genes	Relation type
CCDC92	TF binding region
ENSG00000119242	Chromatin interaction
ENSG00000179195	Chromatin interaction
ENSG00000270095	Chromatin interaction
ENSG00000270061	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10773048	0.96[ASN][1000 genomes]
rs10846579	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10846580	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11057393	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11057394	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11057396	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11057397	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11057399	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11057400	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11057401	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11057407	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11057408	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11057409	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11057412	0.97[EUR][1000 genomes]
rs11057413	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11831913	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11833002	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11835839	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11837287	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1187415	0.95[EUR][1000 genomes]
rs12296259	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12298484	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12301673	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12303671	0.95[EUR][1000 genomes]
rs12303933	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12310367	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12311114	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12311848	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12316080	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12317176	0.94[EUR][1000 genomes]
rs12809125	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12809473	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12823740	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12824567	0.87[EUR][1000 genomes]
rs12827409	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12829951	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12833624	0.96[EUR][1000 genomes]
rs1882491	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2130382	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2178663	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3186071	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34114498	0.97[EUR][1000 genomes]
rs34180676	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34854841	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34878139	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35099862	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35825716	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3789967	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3802999	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4405410	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4575361	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4765127	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4765148	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4765219	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4765305	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4765335	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4765528	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4765541	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4765562	0.97[EUR][1000 genomes]
rs4930721	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4930722	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4930723	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4930724	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4930726	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55990776	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56041971	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6488912	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6488913	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6488914	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7131882	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7132655	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7133378	0.85[EUR][1000 genomes]
rs7134121	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7135314	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71458830	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7301953	0.88[EUR][1000 genomes]
rs7305864	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7307053	0.88[EUR][1000 genomes]
rs7307277	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7311233	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7311969	0.97[EUR][1000 genomes]
rs7312404	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7955815	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7958691	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7961449	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7966192	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7973683	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7975482	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7978610	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs952632	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9863	0.85[EUR][1000 genomes]
rs9971695	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4930725	RP11-380L11.4	cis	Esophagus Muscularis	GTEx
rs4930725	CCDC92	cis	Heart Left Ventricle	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124417600-124443600	Weak transcription	Fetal Kidney	kidney
2	chr12:124417800-124428400	Strong transcription	Brain Germinal Matrix	brain
3	chr12:124418000-124428400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr12:124418000-124431000	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr12:124418200-124430800	Strong transcription	Stomach Smooth Muscle	stomach
6	chr12:124418200-124431400	Strong transcription	Fetal Stomach	stomach
7	chr12:124418600-124430800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr12:124419000-124428400	Strong transcription	Fetal Muscle Leg	muscle
9	chr12:124420200-124433000	Weak transcription	Small Intestine	intestine
10	chr12:124420600-124430800	Strong transcription	Pancreas	Pancrea
11	chr12:124420800-124432600	Weak transcription	HepG2	liver
12	chr12:124421000-124430600	Strong transcription	Skeletal Muscle Male	skeletal muscle
13	chr12:124422400-124439200	Weak transcription	Psoas Muscle	Psoas
14	chr12:124423000-124432800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:124423400-124429800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:124423600-124428200	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr12:124423600-124430600	Strong transcription	Liver	Liver
18	chr12:124423600-124430800	Weak transcription	Dnd41	blood
19	chr12:124423600-124431600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr12:124423600-124442200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr12:124423800-124430600	Strong transcription	Ovary	ovary
22	chr12:124423800-124430600	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr12:124424000-124431200	Strong transcription	Primary T cells from cord blood	blood
24	chr12:124424200-124429200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr12:124424200-124429400	Strong transcription	Left Ventricle	heart
26	chr12:124424200-124430000	Strong transcription	Placenta Amnion	Placenta Amnion
27	chr12:124424200-124430400	Strong transcription	Primary B cells from peripheral blood	blood
28	chr12:124424600-124428600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr12:124424600-124430200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr12:124424800-124430600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:124425200-124428400	Weak transcription	Aorta	Aorta
32	chr12:124425400-124428800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr12:124425600-124428400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr12:124425800-124430400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr12:124425800-124430600	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr12:124426000-124428200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
37	chr12:124426000-124428800	Strong transcription	Rectal Smooth Muscle	rectum
38	chr12:124426000-124430600	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr12:124426200-124428200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:124426200-124428400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr12:124426200-124430800	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr12:124426400-124428600	Enhancers	HUVEC	blood vessel
43	chr12:124426400-124430200	Strong transcription	Colon Smooth Muscle	Colon
44	chr12:124426600-124428400	Weak transcription	Fetal Heart	heart
45	chr12:124426600-124428800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr12:124426600-124428800	Enhancers	HSMMtube	muscle
47	chr12:124426800-124428200	Strong transcription	Colonic Mucosa	Colon
48	chr12:124426800-124428600	Enhancers	NHDF-Ad	bronchial
49	chr12:124426800-124430600	Strong transcription	Duodenum Mucosa	Duodenum
50	chr12:124426800-124436800	Weak transcription	NHLF	lung

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