Variant report

Variant	rs9296291
Chromosome Location	chr6:39056929-39056930
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:39054886..39057587-chr6:39057914..39060553,2	MCF-7	breast:
2	chr6:39056188..39058332-chr6:39081788..39085534,3	MCF-7	breast:
3	chr6:39055895..39057214-chr6:39125035..39125985,4	MCF-7	breast:
4	chr6:39055500..39058719-chr6:39195179..39198658,3	K562	blood:
5	chr6:39056771..39059349-chr6:39083061..39085112,2	K562	blood:
6	chr6:39052982..39054673-chr6:39056335..39058628,2	K562	blood:

Variant related genes	Relation type
ENSG00000164626	Chromatin interaction
ENSG00000112167	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs41273118	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4254984	0.96[ASN][1000 genomes]
rs7696	1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs9462473	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9462475	0.95[ASN][1000 genomes]
rs9462476	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028088	chr6:38821047-39163549	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv538205	chr6:38821047-39163549	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv528286	chr6:39019503-39060478	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1031922	chr6:39034484-39060762	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv462919	chr6:39050384-39062990	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv602963	chr6:39050384-39062990	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9296291	C6orf126	cis	cerebellum	SCAN
rs9296291	PIM1	cis	parietal	SCAN
rs9296291	PI16	cis	cerebellum	SCAN
rs9296291	MRPL2	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39021200-39072000	Weak transcription	Gastric	stomach
2	chr6:39024200-39057800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:39027400-39073000	Weak transcription	Pancreas	Pancrea
4	chr6:39043400-39082000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:39052600-39060400	Enhancers	Fetal Heart	heart
6	chr6:39053000-39072400	Weak transcription	Brain Germinal Matrix	brain
7	chr6:39053400-39057200	Weak transcription	Lung	lung
8	chr6:39053400-39059600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr6:39053800-39058400	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr6:39053800-39058600	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr6:39054000-39057800	Enhancers	Psoas Muscle	Psoas
12	chr6:39054200-39057800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:39054800-39057600	Enhancers	Fetal Muscle Leg	muscle
14	chr6:39055200-39057400	Enhancers	Fetal Lung	lung
15	chr6:39055200-39069800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr6:39055400-39057000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
17	chr6:39055400-39057400	Enhancers	Fetal Stomach	stomach
18	chr6:39055600-39057000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:39055600-39057200	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr6:39055600-39057600	Enhancers	H1 Cell Line	embryonic stem cell
21	chr6:39055600-39060800	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr6:39055800-39057200	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr6:39056000-39057000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr6:39056000-39057000	Enhancers	Rectal Smooth Muscle	rectum
25	chr6:39056400-39057200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr6:39056400-39057400	Enhancers	H9 Cell Line	embryonic stem cell
27	chr6:39056400-39057400	Enhancers	Brain Anterior Caudate	brain
28	chr6:39056600-39058400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:39056600-39058400	Enhancers	Left Ventricle	heart
30	chr6:39056600-39058400	Enhancers	Right Atrium	heart
31	chr6:39056600-39058400	Enhancers	Right Ventricle	heart
32	chr6:39056800-39057400	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr6:39056800-39057400	Enhancers	Stomach Smooth Muscle	stomach
34	chr6:39056800-39057600	Bivalent Enhancer	Fetal Brain Male	brain
35	chr6:39056800-39058200	Weak transcription	Fetal Muscle Trunk	muscle
36	chr6:39056800-39059600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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