Variant report

Variant	rs12209346
Chromosome Location	chr6:36413997-36413998
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36408693..36414213-chr6:36560362..36565197,15	MCF-7	breast:
2	chr6:36403741..36414959-chr6:36560215..36569964,50	K562	blood:
3	chr6:36406846..36414829-chr6:36558734..36566025,43	K562	blood:
4	chr6:36410473..36414235-chr6:36416429..36423107,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240733	Chromatin interaction
ENSG00000112081	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1003250	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10440841	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10947609	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12214285	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12215889	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1570368	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1744654	0.90[ASN][1000 genomes]
rs3752478	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3798471	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4140593	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4711450	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711452	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4711453	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs515129	0.90[ASN][1000 genomes]
rs515186	0.86[ASN][1000 genomes]
rs517890	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs522179	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs544267	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs546272	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs546353	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs547026	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs547966	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs566742	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57389119	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs584196	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs584418	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs595954	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs597153	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs600192	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs605684	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs609067	0.86[ASN][1000 genomes]
rs614028	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs619011	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs621796	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs628213	0.85[ASN][1000 genomes]
rs628314	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs629297	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs629560	0.85[ASN][1000 genomes]
rs629721	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs632943	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6457918	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs659726	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs664370	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6923993	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6941918	0.82[ASN][1000 genomes]
rs73411054	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7744363	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs853873	0.82[ASN][1000 genomes]
rs853881	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853882	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs860513	0.84[ASN][1000 genomes]
rs863815	0.81[ASN][1000 genomes]
rs9296183	0.81[AMR][1000 genomes]
rs9296184	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9357214	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9470274	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9470278	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9470285	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9470309	0.85[ASN][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	nsv885806	chr6:36349890-36621178	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12209346	ETV7	cis	Whole Blood	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36411600-36439800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:36411600-36476400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:36411800-36439400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:36412200-36414800	Weak transcription	Ovary	ovary
5	chr6:36412200-36449200	Weak transcription	Esophagus	oesophagus
6	chr6:36412400-36415000	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr6:36412400-36415200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:36412400-36415200	Weak transcription	Aorta	Aorta
9	chr6:36412400-36416000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:36412400-36416800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:36412400-36416800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:36412400-36416800	Weak transcription	Gastric	stomach
13	chr6:36412400-36437800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:36412400-36438400	Weak transcription	Lung	lung
15	chr6:36412600-36414200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:36412600-36414400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr6:36412600-36414400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr6:36412600-36414400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr6:36412600-36414600	Enhancers	Primary T cells fromperipheralblood	blood
20	chr6:36412600-36414800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:36412600-36415000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:36412600-36415200	Enhancers	Colon Smooth Muscle	Colon
23	chr6:36412600-36415200	Weak transcription	Right Atrium	heart
24	chr6:36412600-36415600	Weak transcription	Thymus	Thymus
25	chr6:36412600-36416200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:36412600-36416200	Weak transcription	Spleen	Spleen
27	chr6:36412600-36416200	Weak transcription	NHLF	lung
28	chr6:36412600-36417400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr6:36412600-36417600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr6:36412600-36418800	Weak transcription	Pancreas	Pancrea
31	chr6:36412600-36420200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr6:36412600-36422800	Weak transcription	Left Ventricle	heart
33	chr6:36412600-36427200	Weak transcription	Fetal Kidney	kidney
34	chr6:36412600-36429600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr6:36412600-36430600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr6:36412600-36430800	Weak transcription	Small Intestine	intestine
37	chr6:36412600-36438600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr6:36412600-36439200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr6:36412600-36449000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr6:36412800-36414200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:36412800-36415000	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr6:36412800-36415000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr6:36412800-36415600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:36412800-36416200	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr6:36412800-36416200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:36412800-36416200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr6:36412800-36416400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr6:36412800-36416800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr6:36412800-36417800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr6:36412800-36418000	Weak transcription	Primary neutrophils fromperipheralblood	blood

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