Variant report

Variant	rs1295391
Chromosome Location	chr6:119675097-119675098
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr6:119675095-119675198	K562	blood:	n/a	n/a
2	MAX	chr6:119674958-119675242	H1-hESC	embryonic stem cell:	n/a	chr6:119675073-119675084
3	MYC	chr6:119674950-119675218	K562	blood:	n/a	chr6:119675073-119675084
4	STAT3	chr6:119674989-119675109	GM12878	blood:	n/a	n/a
5	BHLHE40	chr6:119674903-119675270	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:119674592..119677137-chr6:119682701..119685226,2	K562	blood:
2	chr6:119668152..119672285-chr6:119673337..119678807,6	MCF-7	breast:
3	chr6:119671114..119672646-chr6:119674979..119676830,2	K562	blood:
4	chr6:119671114..119673053-chr6:119674972..119676830,3	K562	blood:
5	chr6:119674592..119678182-chr6:119682701..119685453,4	K562	blood:
6	chr6:119668881..119671932-chr6:119672214..119675857,4	MCF-7	breast:

Variant related genes	Relation type
MAN1A1	TF binding region
ENSG00000111885	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12209570	0.87[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap]
rs1295392	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs195048	0.82[AMR][1000 genomes]
rs195056	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs195058	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs195092	0.89[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs2299878	0.86[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap]
rs2357164	0.86[CEU][hapmap]
rs3778111	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4946406	0.89[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs6937640	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7755155	0.82[CEU][hapmap];0.84[YRI][hapmap]
rs9374788	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9489638	0.85[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025995	chr6:119407742-119709548	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv3447598	chr6:119558591-120119384	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv3389526	chr6:119558598-120190087	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	esv1802628	chr6:119647135-119678881	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1295391	HSS00087597	cis	multi-tissue	Pritchard

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119671800-119689200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:119672400-119675600	Enhancers	Fetal Kidney	kidney
3	chr6:119672400-119675800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr6:119672400-119676200	Enhancers	Primary B cells from cord blood	blood
5	chr6:119673400-119676000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:119673400-119676200	Enhancers	Primary hematopoietic stem cells	blood
7	chr6:119673400-119677200	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr6:119673400-119678200	Weak transcription	NHDF-Ad	bronchial
9	chr6:119673400-119690000	Weak transcription	K562	blood
10	chr6:119673600-119675400	Enhancers	Dnd41	blood
11	chr6:119673600-119680800	Weak transcription	Fetal Heart	heart
12	chr6:119673600-119687200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:119674000-119675400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:119674400-119675200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:119674400-119675200	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr6:119674400-119675200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:119674400-119675200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:119674400-119675200	Enhancers	Brain Anterior Caudate	brain
19	chr6:119674400-119675400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:119674400-119675400	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr6:119674400-119675400	Flanking Active TSS	GM12878-XiMat	blood
22	chr6:119674400-119675600	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr6:119674400-119676000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:119674400-119676000	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr6:119674400-119677600	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr6:119674600-119675200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr6:119674600-119675400	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr6:119674600-119675400	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr6:119674600-119677000	Enhancers	Primary B cells from peripheral blood	blood
30	chr6:119674800-119675600	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr6:119674800-119676400	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr6:119675000-119675200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr6:119675000-119675200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr6:119675000-119675200	Enhancers	H9 Cell Line	embryonic stem cell
35	chr6:119675000-119675200	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr6:119675000-119675200	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr6:119675000-119675400	Enhancers	Rectal Mucosa Donor 31	rectum

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