Variant report

Variant	rs248992
Chromosome Location	chr5:80444191-80444192
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs12659839	0.84[JPT][hapmap]
rs153229	0.88[JPT][hapmap]
rs153231	0.84[JPT][hapmap]
rs153233	0.93[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs153234	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs153235	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs153236	0.93[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs153237	0.82[ASN][1000 genomes]
rs153238	0.82[ASN][1000 genomes]
rs153239	0.89[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs153240	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs153241	0.89[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs153242	0.81[ASN][1000 genomes]
rs153243	0.81[ASN][1000 genomes]
rs153244	0.81[ASN][1000 genomes]
rs168718	0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17213885	0.86[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs173596	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs190339	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs193786	0.93[ASN][1000 genomes]
rs2454870	0.81[ASN][1000 genomes]
rs248980	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs248981	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs248982	0.84[ASN][1000 genomes]
rs248983	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs248984	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs248985	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs248986	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs248987	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs248988	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.80[MKK][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs248989	0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs248990	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs248991	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs26889	0.86[CHD][hapmap];0.90[JPT][hapmap]
rs26890	0.81[ASN][1000 genomes]
rs26891	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs26892	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs26893	0.86[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs26894	0.90[JPT][hapmap]
rs26895	0.86[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs26898	0.86[CHD][hapmap];0.84[JPT][hapmap]
rs27558	0.81[ASN][1000 genomes]
rs27781	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs28820	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34115	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs34116	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs34117	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34120	0.93[ASN][1000 genomes]
rs34121	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs34122	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs382926	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs40046	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs457365	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv830360	chr5:80283278-80446040	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1025799	chr5:80436584-80485252	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80410600-80446600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:80423000-80451400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr5:80424400-80445000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr5:80436800-80448600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:80437400-80447000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:80438800-80445800	Weak transcription	Fetal Muscle Leg	muscle
7	chr5:80438800-80446600	Weak transcription	Fetal Stomach	stomach
8	chr5:80441600-80444400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:80441800-80446600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:80442200-80460800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr5:80442200-80465600	Weak transcription	HepG2	liver
12	chr5:80443400-80444400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr5:80443400-80444400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:80443400-80444400	Enhancers	HSMMtube	muscle
15	chr5:80443600-80444200	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr5:80443600-80444200	Flanking Active TSS	Dnd41	blood
17	chr5:80443600-80444400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr5:80443600-80444400	Enhancers	Brain Hippocampus Middle	brain
19	chr5:80443800-80444200	Active TSS	Primary T cells fromperipheralblood	blood
20	chr5:80443800-80444200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr5:80443800-80444400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr5:80443800-80444400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr5:80443800-80444400	Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr5:80443800-80444400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr5:80443800-80444400	Active TSS	Thymus	Thymus
26	chr5:80444000-80444200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr5:80444000-80444200	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr5:80444000-80444400	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr5:80444000-80444400	Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr5:80444000-80444400	Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr5:80444000-80444400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr5:80444000-80444400	Bivalent Enhancer	NHDF-Ad	bronchial
33	chr5:80444000-80451400	Weak transcription	Ovary	ovary
34	chr5:80444000-80457000	Weak transcription	Brain Cingulate Gyrus	brain

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