Variant report

Variant	rs3186071
Chromosome Location	chr12:124429279-124429280
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:124427289..124429927-chr12:124454570..124456176,2	K562	blood:
2	chr12:124428318..124430502-chr12:124446535..124448670,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270061	Chromatin interaction
ENSG00000270048	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10773048	0.98[ASN][1000 genomes]
rs10846579	0.87[EUR][1000 genomes]
rs10846580	0.90[EUR][1000 genomes]
rs11057393	0.86[EUR][1000 genomes]
rs11057394	0.87[EUR][1000 genomes]
rs11057396	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11057397	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11057399	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11057400	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11057401	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057407	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057408	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11057409	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11057412	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11057413	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11831913	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11833002	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11835839	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837287	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1187415	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12296259	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12298484	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12301673	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12303671	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12303933	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12310367	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12311114	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12311848	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12316080	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12317176	0.87[EUR][1000 genomes]
rs12809125	0.87[EUR][1000 genomes]
rs12809473	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12823740	0.88[ASN][1000 genomes]
rs12824567	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12827409	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12829951	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12833624	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1882491	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2130382	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2178663	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34114498	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34180676	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34854841	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34878139	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35099862	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35825716	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3789967	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3802999	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4405410	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4575361	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4765127	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4765148	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4765219	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4765305	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4765335	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4765528	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4765541	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4765562	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4930721	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4930722	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4930723	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4930724	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4930725	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4930726	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55990776	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56041971	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6488912	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488913	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488914	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7131882	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132655	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7134121	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7135314	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71458830	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7301953	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7305864	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307053	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7307277	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7311233	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7311969	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7312404	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7955815	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7958691	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961449	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7966192	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973683	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975482	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7978610	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs952632	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9863	0.93[EUR][1000 genomes]
rs9971695	0.88[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
rs3186071	RP11-380L11.4	cis	Esophagus Muscularis	GTEx
rs3186071	CCDC92	cis	Heart Left Ventricle	GTEx

Chromatin state (count:102 , 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	chr12:124418000-124431000	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr12:124418200-124430800	Strong transcription	Stomach Smooth Muscle	stomach
4	chr12:124418200-124431400	Strong transcription	Fetal Stomach	stomach
5	chr12:124418600-124430800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr12:124420200-124433000	Weak transcription	Small Intestine	intestine
7	chr12:124420600-124430800	Strong transcription	Pancreas	Pancrea
8	chr12:124420800-124432600	Weak transcription	HepG2	liver
9	chr12:124421000-124430600	Strong transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:124422400-124439200	Weak transcription	Psoas Muscle	Psoas
11	chr12:124423000-124432800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:124423400-124429800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:124423600-124430600	Strong transcription	Liver	Liver
14	chr12:124423600-124430800	Weak transcription	Dnd41	blood
15	chr12:124423600-124431600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:124423600-124442200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr12:124423800-124430600	Strong transcription	Ovary	ovary
18	chr12:124423800-124430600	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr12:124424000-124431200	Strong transcription	Primary T cells from cord blood	blood
20	chr12:124424200-124429400	Strong transcription	Left Ventricle	heart
21	chr12:124424200-124430000	Strong transcription	Placenta Amnion	Placenta Amnion
22	chr12:124424200-124430400	Strong transcription	Primary B cells from peripheral blood	blood
23	chr12:124424600-124430200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr12:124424800-124430600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr12:124425800-124430400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr12:124425800-124430600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr12:124426000-124430600	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr12:124426200-124430800	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr12:124426400-124430200	Strong transcription	Colon Smooth Muscle	Colon
30	chr12:124426800-124430600	Strong transcription	Duodenum Mucosa	Duodenum
31	chr12:124426800-124436800	Weak transcription	NHLF	lung
32	chr12:124427000-124430200	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr12:124427000-124430400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:124427000-124431200	Strong transcription	Spleen	Spleen
35	chr12:124427000-124431400	Strong transcription	Fetal Intestine Small	intestine
36	chr12:124427000-124431600	Strong transcription	Fetal Intestine Large	intestine
37	chr12:124427000-124455000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr12:124427200-124430000	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr12:124427200-124434000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr12:124427200-124436800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr12:124427200-124456200	Weak transcription	Esophagus	oesophagus
42	chr12:124427400-124430000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr12:124427400-124430000	Genic enhancers	Brain Hippocampus Middle	brain
44	chr12:124427400-124436200	Enhancers	Fetal Brain Male	brain
45	chr12:124427600-124430000	Strong transcription	Gastric	stomach
46	chr12:124427600-124430400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:124427600-124430600	Strong transcription	Primary B cells from cord blood	blood
48	chr12:124427600-124430600	Strong transcription	Placenta	Placenta
49	chr12:124427600-124430600	Strong transcription	Thymus	Thymus
50	chr12:124427600-124431200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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