Variant report

Variant	rs7717747
Chromosome Location	chr5:107701188-107701189
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:107699675..107702509-chr5:107715943..107717724,2	K562	blood:
2	chr5:107696924..107698880-chr5:107700620..107702301,2	MCF-7	breast:
3	chr5:107700578..107705838-chr5:107715421..107718628,5	K562	blood:
4	chr5:107700359..107701872-chr5:107716648..107719223,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145743	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10036343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10041907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10063449	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10063866	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs10071595	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10072270	1.00[CEU][hapmap];0.93[YRI][hapmap];0.94[EUR][1000 genomes]
rs10075907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs10455007	0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs11743651	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11744374	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13178456	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1849011	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2029104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs2044709	0.85[EUR][1000 genomes]
rs2044710	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs2112306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2122158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs2167001	0.90[EUR][1000 genomes]
rs2416188	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28497144	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs286764	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs286767	0.80[EUR][1000 genomes]
rs2922423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs2922424	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs2922426	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs2922427	0.90[EUR][1000 genomes]
rs2922428	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs2922429	0.90[EUR][1000 genomes]
rs2922430	0.82[EUR][1000 genomes]
rs2922433	0.87[EUR][1000 genomes]
rs2966795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs2966797	0.90[EUR][1000 genomes]
rs2966799	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs34298471	0.92[EUR][1000 genomes]
rs4541643	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4957553	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4957554	0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs4957751	1.00[CEU][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs4957753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55896795	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57222565	0.92[EUR][1000 genomes]
rs6596770	0.88[CEU][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs6596771	0.81[EUR][1000 genomes]
rs6596777	0.88[EUR][1000 genomes]
rs6870573	0.81[CHD][hapmap]
rs6875297	0.81[ASW][hapmap];1.00[CEU][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs6883082	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs7708996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7726298	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9326725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs962680	0.89[EUR][1000 genomes]
rs989001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	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
4	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
5	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
rs7717747	NCRNA00219	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107615000-107705600	Weak transcription	Left Ventricle	heart
2	chr5:107648000-107704800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr5:107654600-107709400	Weak transcription	Pancreas	Pancrea
4	chr5:107658600-107709200	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr5:107663800-107709400	Weak transcription	Primary T cells from cord blood	blood
6	chr5:107667600-107709200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr5:107668600-107706800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr5:107669200-107708400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr5:107670000-107702400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr5:107675000-107709200	Weak transcription	Fetal Thymus	thymus
11	chr5:107676800-107702400	Weak transcription	Fetal Kidney	kidney
12	chr5:107677800-107709200	Weak transcription	Ovary	ovary
13	chr5:107679200-107706800	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr5:107679800-107705600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr5:107680000-107706800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr5:107680400-107707600	Weak transcription	Fetal Intestine Large	intestine
17	chr5:107682000-107703600	Weak transcription	Dnd41	blood
18	chr5:107683000-107703600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr5:107684400-107702600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr5:107688000-107702600	Weak transcription	Liver	Liver
21	chr5:107688000-107707600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr5:107692000-107702400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr5:107692400-107702400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr5:107693000-107704600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:107693000-107706800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr5:107693600-107706400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr5:107694400-107703400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:107694400-107706800	Weak transcription	GM12878-XiMat	blood
29	chr5:107695000-107702800	Weak transcription	Brain Hippocampus Middle	brain
30	chr5:107695800-107702200	Weak transcription	Small Intestine	intestine
31	chr5:107696600-107709200	Weak transcription	Fetal Lung	lung
32	chr5:107696800-107701200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr5:107697000-107705000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr5:107697200-107715200	Weak transcription	HSMM	muscle
35	chr5:107697400-107703200	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr5:107697600-107705200	Weak transcription	Brain Substantia Nigra	brain
37	chr5:107697600-107706000	Weak transcription	Stomach Mucosa	stomach
38	chr5:107697600-107708000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr5:107697800-107702400	Weak transcription	HSMMtube	muscle
40	chr5:107697800-107703200	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr5:107697800-107707600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:107697800-107709200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr5:107698000-107702400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr5:107698000-107707800	Weak transcription	Brain Anterior Caudate	brain
45	chr5:107698200-107715600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr5:107698800-107703600	Weak transcription	Fetal Muscle Trunk	muscle
47	chr5:107699000-107712800	Weak transcription	Right Ventricle	heart
48	chr5:107699200-107701800	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr5:107699400-107702600	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr5:107699600-107702000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links