Variant report

Variant	rs6676709
Chromosome Location	chr1:214489193-214489194
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:214451643..214456693-chr1:214488650..214497237,17	MCF-7	breast:
2	chr1:214487556..214489408-chr1:214491187..214493754,2	K562	blood:
3	chr1:214489124..214492029-chr1:214494142..214496979,2	MCF-7	breast:
4	chr1:214488324..214490814-chr1:214493702..214496792,3	MCF-7	breast:
5	chr1:214464397..214467228-chr1:214488668..214491420,2	MCF-7	breast:
6	chr1:214454278..214456032-chr1:214487922..214490659,2	K562	blood:
7	chr1:214460531..214463477-chr1:214488827..214490849,2	MCF-7	breast:
8	chr1:214454828..214456756-chr1:214488349..214489973,2	MCF-7	breast:
9	chr1:214461471..214463452-chr1:214488205..214490327,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143499	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1005709	0.86[ASN][1000 genomes]
rs10779613	0.91[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.86[MEX][hapmap];0.86[ASN][1000 genomes]
rs10864092	0.91[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs10864093	0.88[AFR][1000 genomes]
rs11120289	0.86[AFR][1000 genomes]
rs11120290	0.86[ASN][1000 genomes]
rs11120292	0.91[CHB][hapmap];0.85[CHD][hapmap];0.85[ASN][1000 genomes]
rs11120295	0.91[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1134647	0.91[CHB][hapmap];0.85[CHD][hapmap];0.83[ASN][1000 genomes]
rs12024395	0.87[ASN][1000 genomes]
rs12057464	0.85[ASN][1000 genomes]
rs12081918	0.84[AFR][1000 genomes]
rs12124666	0.91[CHB][hapmap];0.85[CHD][hapmap];0.83[ASN][1000 genomes]
rs12725392	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs12737638	0.87[ASW][hapmap];0.98[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs1874804	0.87[ASW][hapmap];0.88[LWK][hapmap];0.80[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs2270704	0.91[CHB][hapmap];0.83[CHD][hapmap];0.85[ASN][1000 genomes]
rs2291830	0.91[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs34932055	0.94[AFR][1000 genomes]
rs3754136	0.87[ASW][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes]
rs3767843	0.95[LWK][hapmap];0.89[MKK][hapmap];0.85[AFR][1000 genomes]
rs4655242	0.86[CHB][hapmap]
rs4655245	0.91[CHB][hapmap];0.85[CHD][hapmap];0.85[ASN][1000 genomes]
rs4655335	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs6540817	0.91[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.86[MEX][hapmap];0.85[ASN][1000 genomes]
rs6540818	0.86[ASN][1000 genomes]
rs6540819	0.91[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.86[MEX][hapmap];0.86[ASN][1000 genomes]
rs6540820	0.87[ASN][1000 genomes]
rs6540821	0.91[CHB][hapmap];0.85[CHD][hapmap];0.84[ASN][1000 genomes]
rs6540822	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs6660940	0.84[ASN][1000 genomes]
rs6662275	0.87[ASN][1000 genomes]
rs6662864	0.91[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs6665343	0.91[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.86[MEX][hapmap];0.87[ASN][1000 genomes]
rs6670066	0.82[ASN][1000 genomes]
rs6673096	0.83[ASN][1000 genomes]
rs6687411	0.95[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs6691083	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs6700976	0.91[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.86[MEX][hapmap];0.87[ASN][1000 genomes]
rs6701764	0.91[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs7419021	0.91[CHB][hapmap];0.85[CHD][hapmap]
rs7512745	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs870117	0.87[ASW][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes]
rs9429915	0.82[ASN][1000 genomes]
rs9429918	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs9970083	0.82[CHB][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6676709	SMYD2	cis	lymphoblastoid	seeQTL
rs6676709	SMYD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:214456400-214491800	Weak transcription	Pancreas	Pancrea
2	chr1:214459200-214491400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr1:214462000-214491800	Weak transcription	NHEK	skin
4	chr1:214471000-214489400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:214471000-214517400	Weak transcription	Fetal Kidney	kidney
6	chr1:214476600-214492200	Weak transcription	K562	blood
7	chr1:214477000-214489800	Weak transcription	NH-A	brain
8	chr1:214477200-214491600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:214477200-214492200	Weak transcription	Aorta	Aorta
10	chr1:214477400-214489800	Weak transcription	NHLF	lung
11	chr1:214477400-214492200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:214477400-214506400	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:214477400-214506400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:214477400-214511000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:214478800-214491800	Weak transcription	Spleen	Spleen
16	chr1:214478800-214492200	Weak transcription	Esophagus	oesophagus
17	chr1:214479000-214503000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:214479200-214491800	Weak transcription	Lung	lung
19	chr1:214479400-214493000	Enhancers	Fetal Heart	heart
20	chr1:214479800-214490000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:214480200-214490800	Weak transcription	Fetal Intestine Small	intestine
22	chr1:214482200-214510600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:214483000-214490400	Enhancers	Liver	Liver
24	chr1:214483600-214492200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:214483600-214501600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:214483800-214489800	Weak transcription	Osteobl	bone
27	chr1:214484000-214490000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:214484400-214499800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr1:214484400-214510800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:214484600-214490600	Weak transcription	GM12878-XiMat	blood
31	chr1:214484800-214491800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr1:214484800-214492200	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr1:214484800-214501800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr1:214484800-214507800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr1:214484800-214522000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr1:214485000-214491200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:214485000-214492200	Weak transcription	Fetal Brain Female	brain
38	chr1:214485000-214506400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr1:214485000-214513200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr1:214485600-214499600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:214485800-214499600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:214486000-214490000	Weak transcription	HSMM	muscle
43	chr1:214486000-214492400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr1:214486200-214491600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:214486200-214526000	Weak transcription	Psoas Muscle	Psoas
46	chr1:214486400-214489400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:214486400-214489600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:214486400-214490000	Strong transcription	HepG2	liver
49	chr1:214486600-214489800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr1:214486800-214489800	Weak transcription	Placenta Amnion	Placenta Amnion

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