Variant report

Variant	rs6875297
Chromosome Location	chr5:107688854-107688855
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:107687278..107689541-chr5:107694592..107696182,2	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10036343	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10041907	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10063449	0.92[EUR][1000 genomes]
rs10063866	0.86[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs10071595	0.88[EUR][1000 genomes]
rs10072270	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10075907	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10463586	0.82[EUR][1000 genomes]
rs11743651	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs11744374	0.94[EUR][1000 genomes]
rs13178456	0.94[EUR][1000 genomes]
rs1849011	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2029104	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2044709	0.81[EUR][1000 genomes]
rs2044710	1.00[CEU][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs2112306	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2122158	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2167001	0.86[EUR][1000 genomes]
rs2416188	1.00[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs28497144	0.94[EUR][1000 genomes]
rs286764	0.96[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes]
rs286767	0.84[EUR][1000 genomes]
rs2922423	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2922424	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2922426	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2922427	0.86[EUR][1000 genomes]
rs2922428	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2922429	0.86[EUR][1000 genomes]
rs2922433	0.83[EUR][1000 genomes]
rs2966795	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2966797	0.86[EUR][1000 genomes]
rs2966799	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs34298471	0.88[EUR][1000 genomes]
rs4541643	1.00[CEU][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs4957553	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs4957751	0.81[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4957753	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs55896795	0.92[EUR][1000 genomes]
rs57222565	0.88[EUR][1000 genomes]
rs6596770	0.88[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs6596771	0.84[EUR][1000 genomes]
rs6596777	0.84[EUR][1000 genomes]
rs6883082	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs7708996	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7713705	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs7717747	0.81[ASW][hapmap];1.00[CEU][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs7726298	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9326725	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs962680	0.85[EUR][1000 genomes]
rs989001	1.00[CEU][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882683	chr5:107476501-107769095	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv882684	chr5:107521677-107695558	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv830442	chr5:107539150-107697020	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv882685	chr5:107564746-107695558	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv882686	chr5:107564746-107769095	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv882687	chr5:107595383-107695558	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv882688	chr5:107595383-107715746	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	esv2755544	chr5:107614101-107748101	Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6875297	NCRNA00219	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107615000-107705600	Weak transcription	Left Ventricle	heart
2	chr5:107639800-107697200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:107648000-107704800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr5:107654600-107709400	Weak transcription	Pancreas	Pancrea
5	chr5:107658600-107709200	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr5:107659400-107700000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr5:107661800-107696400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:107663800-107709400	Weak transcription	Primary T cells from cord blood	blood
9	chr5:107667600-107709200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr5:107668600-107706800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr5:107668800-107699600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr5:107669200-107708400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr5:107669400-107700400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr5:107670000-107702400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr5:107675000-107709200	Weak transcription	Fetal Thymus	thymus
16	chr5:107675800-107700000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr5:107676000-107696200	Weak transcription	Fetal Lung	lung
18	chr5:107676800-107702400	Weak transcription	Fetal Kidney	kidney
19	chr5:107677400-107700800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:107677800-107700400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:107677800-107709200	Weak transcription	Ovary	ovary
22	chr5:107678400-107699800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:107679200-107706800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr5:107679600-107699800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:107679800-107696800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr5:107679800-107705600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr5:107680000-107706800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr5:107680400-107707600	Weak transcription	Fetal Intestine Large	intestine
29	chr5:107680600-107690000	Weak transcription	Fetal Intestine Small	intestine
30	chr5:107680800-107697400	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr5:107681400-107693600	Weak transcription	GM12878-XiMat	blood
32	chr5:107681600-107699800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr5:107682000-107703600	Weak transcription	Dnd41	blood
34	chr5:107683000-107703600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr5:107683400-107697200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:107684400-107699800	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr5:107684400-107702600	Weak transcription	Primary B cells from peripheral blood	blood
38	chr5:107686200-107701000	Weak transcription	Adipose Nuclei	Adipose
39	chr5:107688000-107696800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr5:107688000-107702600	Weak transcription	Liver	Liver
41	chr5:107688000-107707600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr5:107688600-107689000	Strong transcription	Primary B cells from cord blood	blood

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