Variant report

Variant	rs6895741
Chromosome Location	chr5:154203264-154203265
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1035368	1.00[TSI][hapmap]
rs10515727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12186480	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12186610	0.84[EUR][1000 genomes]
rs12187572	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12187890	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12187921	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12187934	0.82[ASN][1000 genomes]
rs12187974	0.85[ASN][1000 genomes]
rs12188149	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12188498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12188906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12189508	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12300	0.90[TSI][hapmap]
rs1421813	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1421814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1421815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1421819	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17096232	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17116409	1.00[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs17116417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17116421	1.00[TSI][hapmap]
rs17116433	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes]
rs17116442	1.00[TSI][hapmap]
rs17116455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17116489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17116534	1.00[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs17116638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17116669	0.82[ASN][1000 genomes]
rs17116707	1.00[JPT][hapmap]
rs1974776	1.00[TSI][hapmap]
rs1974777	1.00[TSI][hapmap]
rs2047305	1.00[JPT][hapmap]
rs2112223	1.00[CHB][hapmap]
rs2258437	1.00[TSI][hapmap]
rs2291780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2544880	1.00[TSI][hapmap]
rs2544884	1.00[TSI][hapmap]
rs2644743	1.00[TSI][hapmap]
rs2644744	1.00[CHB][hapmap];1.00[TSI][hapmap]
rs2688198	1.00[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs2688201	1.00[TSI][hapmap]
rs2688208	1.00[CHB][hapmap]
rs28372688	0.85[ASN][1000 genomes]
rs348739	1.00[TSI][hapmap]
rs348750	1.00[TSI][hapmap]
rs348752	1.00[TSI][hapmap]
rs3776984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs39614	1.00[TSI][hapmap]
rs4452598	0.86[EUR][1000 genomes]
rs4626377	0.86[EUR][1000 genomes]
rs55692274	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56773390	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56895891	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61145644	0.82[ASN][1000 genomes]
rs6580123	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6865950	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6871813	0.82[ASN][1000 genomes]
rs6895588	0.82[ASN][1000 genomes]
rs6895702	0.82[ASN][1000 genomes]
rs6895742	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs702742	1.00[TSI][hapmap]
rs73806917	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73807206	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73807207	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73807213	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73807216	0.82[ASN][1000 genomes]
rs73809507	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7709899	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7716019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs816717	1.00[TSI][hapmap]
rs816718	1.00[CHB][hapmap];0.95[TSI][hapmap]
rs816720	1.00[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830521	chr5:154147567-154244266	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154169200-154204200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
2	chr5:154169200-154204200	Strong transcription	Dnd41	blood
3	chr5:154169400-154204000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:154169400-154204200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr5:154169400-154204200	Strong transcription	Duodenum Mucosa	Duodenum
6	chr5:154169400-154205800	Strong transcription	Skeletal Muscle Female	skeletal muscle
7	chr5:154169600-154204200	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr5:154174000-154212200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:154174800-154204400	Strong transcription	Placenta	Placenta
10	chr5:154175200-154204400	Strong transcription	Osteobl	bone
11	chr5:154175200-154204600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:154178200-154204000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:154181000-154211600	Strong transcription	Brain Hippocampus Middle	brain
14	chr5:154181200-154204800	Strong transcription	Brain Cingulate Gyrus	brain
15	chr5:154182000-154211400	Strong transcription	Left Ventricle	heart
16	chr5:154187000-154211400	Strong transcription	Fetal Stomach	stomach
17	chr5:154187600-154204200	Strong transcription	Skeletal Muscle Male	skeletal muscle
18	chr5:154187600-154204400	Strong transcription	Brain Germinal Matrix	brain
19	chr5:154189400-154206000	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr5:154189800-154204600	Strong transcription	Lung	lung
21	chr5:154190400-154204200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr5:154191600-154208600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:154191800-154206200	Strong transcription	Brain Anterior Caudate	brain
24	chr5:154191800-154211600	Strong transcription	Adipose Nuclei	Adipose
25	chr5:154192400-154204200	Strong transcription	Brain Substantia Nigra	brain
26	chr5:154193000-154211800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr5:154193800-154204200	Strong transcription	Fetal Thymus	thymus
28	chr5:154194000-154209400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr5:154195600-154204600	Strong transcription	A549	lung
30	chr5:154195600-154208000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr5:154195600-154214400	Weak transcription	Small Intestine	intestine
32	chr5:154196000-154203600	Strong transcription	Liver	Liver
33	chr5:154196000-154229200	Weak transcription	Psoas Muscle	Psoas
34	chr5:154196400-154214000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr5:154196600-154208000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr5:154196800-154207400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr5:154197000-154204200	Strong transcription	Brain Angular Gyrus	brain
38	chr5:154197400-154203600	Weak transcription	NH-A	brain
39	chr5:154197600-154203400	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr5:154197600-154208400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr5:154197600-154214400	Weak transcription	HUVEC	blood vessel
42	chr5:154197800-154214400	Weak transcription	Hela-S3	cervix
43	chr5:154198200-154204400	Strong transcription	Ovary	ovary
44	chr5:154198400-154207200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr5:154198600-154204200	Strong transcription	Rectal Smooth Muscle	rectum
46	chr5:154198600-154204400	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr5:154198600-154205800	Strong transcription	Colon Smooth Muscle	Colon
48	chr5:154198600-154206400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr5:154198600-154211200	Strong transcription	Stomach Smooth Muscle	stomach
50	chr5:154198600-154211400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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