Variant report

Variant	rs2295840
Chromosome Location	chr6:80724156-80724157
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10943681	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10943682	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10943688	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1205578	0.95[ASN][1000 genomes]
rs1205579	0.84[JPT][hapmap]
rs12526265	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1410521	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1410522	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs151642	0.93[ASN][1000 genomes]
rs151645	0.83[ASN][1000 genomes]
rs151657	0.93[ASN][1000 genomes]
rs151658	0.84[JPT][hapmap]
rs151660	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs151663	0.84[JPT][hapmap]
rs151664	0.84[JPT][hapmap]
rs1897870	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1927425	0.83[CEU][hapmap];0.87[CHB][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1927426	0.83[CEU][hapmap];0.87[CHB][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2149082	0.83[EUR][1000 genomes]
rs2181070	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2295838	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2295841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs239495	0.84[ASN][1000 genomes]
rs239497	0.91[ASN][1000 genomes]
rs239500	0.93[ASN][1000 genomes]
rs239552	0.84[JPT][hapmap]
rs239554	0.83[JPT][hapmap]
rs239555	0.84[JPT][hapmap]
rs239558	0.84[JPT][hapmap]
rs239560	0.91[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs239572	0.84[JPT][hapmap]
rs239578	0.93[ASN][1000 genomes]
rs239582	0.86[JPT][hapmap]
rs239583	0.94[JPT][hapmap]
rs239587	0.84[JPT][hapmap]
rs240212	0.84[JPT][hapmap]
rs240213	0.92[JPT][hapmap]
rs240214	0.95[ASN][1000 genomes]
rs240216	0.84[JPT][hapmap]
rs240217	0.95[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs240218	0.95[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs240228	0.84[JPT][hapmap]
rs240229	0.84[JPT][hapmap]
rs2757084	0.93[ASN][1000 genomes]
rs2769337	0.95[ASN][1000 genomes]
rs3799497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3812151	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3967160	0.81[EUR][1000 genomes]
rs465483	0.96[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4706108	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4706826	0.91[ASN][1000 genomes]
rs4706827	0.83[CHB][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs587984	0.95[ASN][1000 genomes]
rs61795	0.84[JPT][hapmap]
rs61796	0.84[JPT][hapmap]
rs652752	0.95[ASN][1000 genomes]
rs653665	0.84[JPT][hapmap]
rs666040	0.96[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs6925415	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9294168	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9341801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9341802	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9341803	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9343961	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9343965	0.83[CEU][hapmap];0.87[CHB][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs9350843	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs9352790	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9352797	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9359406	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9448877	0.92[ASN][1000 genomes]
rs9448880	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv5370	chr6:80715351-80751740	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80714800-80738800	Weak transcription	Small Intestine	intestine
2	chr6:80715000-80730400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:80715000-80748000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:80715000-80752200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:80715000-80752400	Weak transcription	Placenta	Placenta
6	chr6:80715200-80726000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr6:80715200-80727000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr6:80715200-80730800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:80715200-80734000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:80715200-80734400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:80715200-80739200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr6:80715200-80749600	Weak transcription	Fetal Intestine Small	intestine
13	chr6:80715200-80752000	Weak transcription	Primary B cells from cord blood	blood
14	chr6:80715200-80752200	Weak transcription	Primary T cells from cord blood	blood
15	chr6:80715400-80726000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:80715400-80727000	Weak transcription	Fetal Muscle Leg	muscle
17	chr6:80715400-80729400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr6:80715400-80742200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:80715400-80743200	Weak transcription	Brain Germinal Matrix	brain
20	chr6:80715400-80745400	Weak transcription	Fetal Lung	lung
21	chr6:80715400-80755000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr6:80715400-80756800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:80715600-80724600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr6:80715600-80725200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:80715600-80739200	Weak transcription	Fetal Stomach	stomach
26	chr6:80715600-80754400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr6:80715600-80763800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr6:80715800-80733400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:80715800-80753600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr6:80715800-80753800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr6:80715800-80754400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr6:80716000-80726000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:80716000-80728600	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr6:80716000-80729400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:80716000-80739200	Weak transcription	NHEK	skin
36	chr6:80716000-80743600	Weak transcription	Fetal Heart	heart
37	chr6:80716200-80725200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:80716200-80727800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr6:80716200-80728000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:80716200-80754600	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr6:80716400-80727800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:80716800-80753600	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr6:80717000-80728000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:80717400-80724800	Strong transcription	NH-A	brain
45	chr6:80717400-80727400	Strong transcription	HUVEC	blood vessel
46	chr6:80717400-80728000	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr6:80717400-80739200	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr6:80717600-80724600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr6:80717600-80726800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:80717600-80727800	Strong transcription	HSMM	muscle

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