Variant report

Variant	rs12525580
Chromosome Location	chr6:74288782-74288783
allele	C/G
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:74288220..74292842-chr6:74293561..74299022,14	K562	blood:
2	chr6:74224085..74235157-chr6:74287002..74297560,44	MCF-7	breast:
3	chr6:74269117..74271723-chr6:74288666..74291103,2	K562	blood:
4	chr6:74287302..74289966-chr6:74361696..74364056,2	MCF-7	breast:
5	chr6:74273534..74278713-chr6:74287099..74290342,5	K562	blood:
6	chr6:74287590..74292040-chr6:74293648..74296536,4	MCF-7	breast:
7	chr6:74220978..74235626-chr6:74283533..74299827,68	K562	blood:
8	chr6:74288307..74290175-chr6:74362549..74365093,2	K562	blood:
9	chr6:74287356..74290171-chr6:74314710..74316586,2	MCF-7	breast:
10	chr6:74273534..74277710-chr6:74287099..74290160,5	K562	blood:
11	chr6:74278735..74283200-chr6:74288390..74290564,5	K562	blood:
12	chr6:74222492..74235445-chr6:74283533..74292948,42	K562	blood:
13	chr6:74223949..74234010-chr6:74285694..74297775,46	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000229862	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000119899	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12528608	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34485415	0.83[EUR][1000 genomes]
rs6910702	0.84[EUR][1000 genomes]
rs6931449	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9446932	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv886158	chr6:74126084-74436825	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
3	nsv1027968	chr6:74155378-74521923	Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	nsv538305	chr6:74155378-74521923	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv1017716	chr6:74173173-74401162	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
6	nsv1023250	chr6:74189642-74605976	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
7	nsv538306	chr6:74189642-74605976	Strong transcription Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
8	nsv463153	chr6:74229258-74290291	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
9	nsv603693	chr6:74229258-74290291	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
10	nsv527357	chr6:74253266-74325403	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv603694	chr6:74275405-74365807	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12525580	EEF1A1	cis	cerebellum	SCAN
rs12525580	EEF1A1	cis	parietal	SCAN
rs12525580	C6orf221	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74281200-74288800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:74281200-74289000	Weak transcription	Psoas Muscle	Psoas
3	chr6:74285000-74289000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:74285400-74289200	Weak transcription	Small Intestine	intestine
5	chr6:74287000-74289600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr6:74287200-74289200	Enhancers	A549	lung
7	chr6:74287200-74289400	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr6:74287200-74289600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:74287200-74289600	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr6:74287200-74289600	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr6:74287200-74289800	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr6:74287200-74289800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr6:74287200-74289800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:74287200-74290000	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr6:74287200-74290800	Enhancers	Fetal Heart	heart
16	chr6:74287400-74289000	Enhancers	Hela-S3	cervix
17	chr6:74287400-74289000	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr6:74287400-74289200	Enhancers	HepG2	liver
19	chr6:74287400-74289200	Enhancers	NHDF-Ad	bronchial
20	chr6:74287400-74289200	Enhancers	NHLF	lung
21	chr6:74287400-74289600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:74287400-74289600	Enhancers	Placenta Amnion	Placenta Amnion
23	chr6:74287400-74290000	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr6:74287400-74290000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:74287400-74290000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:74287400-74290000	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr6:74287400-74290000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:74287400-74290200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:74287400-74290400	Enhancers	H1 Cell Line	embryonic stem cell
30	chr6:74287400-74290400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:74287600-74289000	Weak transcription	Stomach Mucosa	stomach
32	chr6:74287600-74289600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:74287600-74290000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:74287600-74290000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr6:74287600-74290000	Enhancers	Fetal Intestine Small	intestine
36	chr6:74287600-74290200	Enhancers	Liver	Liver
37	chr6:74287800-74288800	Weak transcription	Right Atrium	heart
38	chr6:74287800-74289000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:74287800-74289000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr6:74287800-74289200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:74287800-74289200	Enhancers	GM12878-XiMat	blood
42	chr6:74287800-74289600	Enhancers	K562	blood
43	chr6:74287800-74289800	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr6:74287800-74290000	Enhancers	Duodenum Mucosa	Duodenum
45	chr6:74287800-74290000	Enhancers	Placenta	Placenta
46	chr6:74288000-74289000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr6:74288000-74289000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:74288000-74289200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr6:74288000-74289600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr6:74288000-74296000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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