Variant report

Variant	rs6839123
Chromosome Location	chr4:147105438-147105439
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:147099369..147101389-chr4:147104400..147106028,2	MCF-7	breast:

Extended variants
information (count: 112 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10000407	0.83[EUR][1000 genomes]
rs10017509	0.83[CEU][hapmap]
rs10519776	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1079476	0.98[ASN][1000 genomes]
rs11100919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721367	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721873	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11722991	0.83[CEU][hapmap]
rs11723069	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11724307	0.85[EUR][1000 genomes]
rs11725678	0.81[EUR][1000 genomes]
rs11728525	0.85[EUR][1000 genomes]
rs11728609	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11730306	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11733347	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734320	0.83[CEU][hapmap]
rs11940961	0.92[CEU][hapmap];0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs12152657	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152692	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12186313	0.83[CEU][hapmap]
rs17021186	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17021217	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17021239	0.81[CEU][hapmap]
rs17021241	0.82[CEU][hapmap]
rs17756056	0.83[EUR][1000 genomes]
rs17756234	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17757522	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17757685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17757715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17758092	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17758396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17758420	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814023	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814598	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864371	0.92[CEU][hapmap];0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs1865531	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2007366	0.83[EUR][1000 genomes]
rs2068009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115796	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115797	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164280	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28393640	0.81[EUR][1000 genomes]
rs28420466	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733458	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733459	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3733460	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3733461	0.83[CEU][hapmap]
rs3756081	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756082	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756083	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775498	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815967	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3948408	0.81[EUR][1000 genomes]
rs4282199	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4549398	0.81[EUR][1000 genomes]
rs4835283	0.83[CEU][hapmap]
rs4835284	0.83[CEU][hapmap]
rs4835286	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs55736910	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56174047	0.85[EUR][1000 genomes]
rs56279747	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56289966	0.81[EUR][1000 genomes]
rs56333123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56393662	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs62326764	0.81[EUR][1000 genomes]
rs62326797	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62326801	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62326802	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62326804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62326848	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537399	0.81[EUR][1000 genomes]
rs6537400	0.83[EUR][1000 genomes]
rs6537401	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537402	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6537403	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6813969	0.81[CEU][hapmap]
rs6815527	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816161	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6820462	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821066	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821444	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821479	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821863	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824313	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6832576	0.83[EUR][1000 genomes]
rs6838174	0.84[CEU][hapmap]
rs6838458	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6839141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843421	0.81[CEU][hapmap]
rs6844381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847511	0.85[YRI][hapmap]
rs6856647	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6858813	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72727922	0.81[EUR][1000 genomes]
rs72727944	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72727952	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7657269	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662843	0.81[LWK][hapmap];0.87[YRI][hapmap]
rs7665079	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695415	0.83[EUR][1000 genomes]
rs7745	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919482	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919483	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308199	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][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	nsv461674	chr4:147047072-147143572	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv595650	chr4:147047072-147143572	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1018859	chr4:147055618-147138397	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6839123	LSM6	cis	parietal	SCAN
rs6839123	LSM6	cis	cerebellum	SCAN
rs6839123	RP11-6L6.2	cis	Skin Sun Exposed Lower leg	GTEx
rs6839123	RP11-6L6.2	cis	Nerve Tibial	GTEx
rs6839123	RP11-6L6.2	cis	Adipose Subcutaneous	GTEx
rs6839123	RP11-6L6.2	cis	lung	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147097600-147108800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:147097800-147108600	Weak transcription	HSMMtube	muscle
3	chr4:147097800-147108800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:147097800-147108800	Weak transcription	Esophagus	oesophagus
5	chr4:147097800-147111000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr4:147097800-147115400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:147098400-147107400	Weak transcription	HSMM	muscle
8	chr4:147098400-147107800	Weak transcription	Fetal Kidney	kidney
9	chr4:147098400-147108000	Weak transcription	NH-A	brain
10	chr4:147098400-147108800	Weak transcription	NHLF	lung
11	chr4:147098400-147111400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:147098400-147118600	Weak transcription	Colonic Mucosa	Colon
13	chr4:147098600-147105800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr4:147098600-147107800	Weak transcription	HMEC	breast
15	chr4:147098600-147113800	Weak transcription	Hela-S3	cervix
16	chr4:147099000-147108400	Weak transcription	Aorta	Aorta
17	chr4:147099200-147107400	Weak transcription	Osteobl	bone
18	chr4:147099200-147107600	Weak transcription	Brain Germinal Matrix	brain
19	chr4:147099400-147107800	Weak transcription	Thymus	Thymus
20	chr4:147099400-147108000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr4:147099400-147108200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr4:147099400-147109400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:147100000-147107800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr4:147100200-147107800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr4:147100200-147108800	Weak transcription	Fetal Stomach	stomach
26	chr4:147100200-147108800	Weak transcription	HUVEC	blood vessel
27	chr4:147101200-147108200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr4:147101200-147108800	Weak transcription	Fetal Brain Female	brain
29	chr4:147101400-147107800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr4:147101400-147107800	Weak transcription	HepG2	liver
31	chr4:147101400-147108000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr4:147101400-147108200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:147101400-147108800	Weak transcription	Spleen	Spleen
34	chr4:147101400-147111400	Weak transcription	Right Ventricle	heart
35	chr4:147101400-147114000	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr4:147101400-147116200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr4:147101600-147107200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr4:147101600-147107400	Weak transcription	Brain Substantia Nigra	brain
39	chr4:147101600-147107600	Weak transcription	Brain Anterior Caudate	brain
40	chr4:147101600-147107600	Weak transcription	Left Ventricle	heart
41	chr4:147101600-147107800	Weak transcription	Psoas Muscle	Psoas
42	chr4:147101600-147108000	Weak transcription	Colon Smooth Muscle	Colon
43	chr4:147101600-147108000	Weak transcription	Stomach Smooth Muscle	stomach
44	chr4:147101600-147108200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr4:147101600-147108400	Weak transcription	NHEK	skin
46	chr4:147101600-147108800	Weak transcription	Lung	lung
47	chr4:147101600-147108800	Weak transcription	Pancreas	Pancrea
48	chr4:147101600-147109400	Weak transcription	Fetal Intestine Small	intestine
49	chr4:147101600-147109400	Weak transcription	Gastric	stomach
50	chr4:147101600-147109800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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