Variant report

Variant	rs2394049
Chromosome Location	chr6:28239681-28239682
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28232169..28234255-chr6:28237329..28239836,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1005125	1.00[YRI][hapmap]
rs1052215	0.95[CHB][hapmap];1.00[YRI][hapmap]
rs1150668	0.91[JPT][hapmap]
rs1150694	0.91[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1150705	0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1150707	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1150709	0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1150711	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1150716	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1150718	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1150721	1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1150724	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1150726	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12214383	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1225618	0.90[JPT][hapmap]
rs1225710	0.86[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs1225715	0.90[JPT][hapmap]
rs1233660	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1233713	0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13408	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1531681	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1654774	0.86[JPT][hapmap]
rs1736891	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1736895	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1736904	0.80[CHB][hapmap]
rs1778484	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1997660	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2021826	0.91[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs203869	0.86[JPT][hapmap]
rs203878	0.86[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs213236	0.80[CHB][hapmap]
rs213238	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs213240	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2142730	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2531806	0.82[AFR][1000 genomes]
rs2622320	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs2622322	0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs2791333	0.89[AFR][1000 genomes]
rs2859348	0.91[CHB][hapmap]
rs34024998	0.83[EUR][1000 genomes]
rs4713158	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs707907	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs7206	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs853683	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs853684	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs853690	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs853693	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9301	0.95[CHB][hapmap];0.80[JPT][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9468333	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.84[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	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs2394049	AL022393.7	cis	Heart Left Ventricle	GTEx
rs2394049	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs2394049	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs2394049	AL022393.7	cis	Esophagus Muscularis	GTEx
rs2394049	AL022393.7	cis	Muscle Skeletal	GTEx
rs2394049	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs2394049	ZSCAN31	cis	Esophagus Muscularis	GTEx
rs2394049	RP5-874C20.3	cis	Thyroid	GTEx
rs2394049	ZSCAN31	cis	Skin Sun Exposed Lower leg	GTEx
rs2394049	ZSCAN31	cis	Muscle Skeletal	GTEx
rs2394049	ZSCAN31	cis	Thyroid	GTEx
rs2394049	AL022393.7	cis	Nerve Tibial	GTEx
rs2394049	ZSCAN31	cis	lung	GTEx
rs2394049	TRIM27	cis	Skin Sun Exposed Lower leg	GTEx
rs2394049	ZSCAN23	cis	Artery Tibial	GTEx
rs2394049	AL022393.7	cis	Artery Tibial	GTEx
rs2394049	ZSCAN23	cis	Muscle Skeletal	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28235400-28249000	Weak transcription	Small Intestine	intestine
2	chr6:28235600-28239800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:28235600-28239800	Weak transcription	Pancreas	Pancrea
4	chr6:28235600-28240000	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr6:28235600-28243400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:28235600-28249000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:28235600-28249000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:28236000-28239800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr6:28236000-28239800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr6:28236000-28239800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:28236200-28239800	Weak transcription	Liver	Liver
12	chr6:28236200-28239800	Weak transcription	Colonic Mucosa	Colon
13	chr6:28236200-28239800	Weak transcription	HSMM	muscle
14	chr6:28236200-28240000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:28236200-28241800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr6:28236200-28247400	Weak transcription	Stomach Mucosa	stomach
17	chr6:28236200-28248000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr6:28236200-28249400	Weak transcription	Fetal Heart	heart
19	chr6:28236400-28239800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr6:28236400-28239800	Weak transcription	Fetal Kidney	kidney
21	chr6:28236400-28239800	Weak transcription	HSMMtube	muscle
22	chr6:28236400-28239800	Weak transcription	NHLF	lung
23	chr6:28236400-28240200	Weak transcription	Fetal Lung	lung
24	chr6:28236400-28240400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr6:28236400-28240400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:28236400-28240400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr6:28236400-28242000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr6:28236800-28240600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr6:28237000-28240200	Weak transcription	Fetal Brain Male	brain
30	chr6:28237400-28239800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:28237400-28239800	Weak transcription	Brain Angular Gyrus	brain
32	chr6:28237400-28239800	Weak transcription	Osteobl	bone
33	chr6:28237400-28241600	Weak transcription	GM12878-XiMat	blood
34	chr6:28237400-28245800	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr6:28237400-28249000	Weak transcription	Psoas Muscle	Psoas
36	chr6:28237600-28239800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr6:28237600-28248800	Weak transcription	A549	lung
38	chr6:28237800-28239800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:28237800-28239800	Weak transcription	NHEK	skin
40	chr6:28238000-28240200	Weak transcription	NH-A	brain
41	chr6:28238000-28245600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:28238000-28248800	Weak transcription	Hela-S3	cervix
43	chr6:28238200-28239800	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr6:28238200-28239800	Weak transcription	NHDF-Ad	bronchial
45	chr6:28238200-28245200	Strong transcription	Fetal Intestine Large	intestine
46	chr6:28238400-28239800	Weak transcription	K562	blood
47	chr6:28238800-28244000	Strong transcription	Ovary	ovary
48	chr6:28238800-28245400	Strong transcription	Fetal Stomach	stomach
49	chr6:28238800-28245600	Strong transcription	Primary T cells from cord blood	blood
50	chr6:28238800-28245800	Strong transcription	Fetal Muscle Trunk	muscle

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