Variant report

Variant	rs7695415
Chromosome Location	chr4:147056235-147056236
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:147055908..147058873-chr4:147059749..147061908,2	K562	blood:
2	chr4:147055512..147057408-chr4:147060408..147062142,2	K562	blood:

Extended variants
information (count: 91 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10000407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10017509	0.88[CEU][hapmap]
rs10519776	0.83[EUR][1000 genomes]
rs11100919	0.83[EUR][1000 genomes]
rs11721873	0.83[EUR][1000 genomes]
rs11722991	0.88[CEU][hapmap]
rs11723069	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11724307	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11725678	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11728525	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11728609	0.83[EUR][1000 genomes]
rs11729787	0.83[EUR][1000 genomes]
rs11730306	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11733347	0.83[EUR][1000 genomes]
rs11734320	0.88[CEU][hapmap]
rs11940961	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12152657	0.83[EUR][1000 genomes]
rs12152709	0.83[EUR][1000 genomes]
rs12186313	0.88[CEU][hapmap]
rs17021106	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17021186	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[MEX][hapmap]
rs17021217	0.83[EUR][1000 genomes]
rs17021239	0.85[CEU][hapmap]
rs17021241	0.86[CEU][hapmap]
rs17756056	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17756234	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17757522	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs17757685	0.96[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs17757715	0.83[EUR][1000 genomes]
rs17758092	0.83[EUR][1000 genomes]
rs17758396	0.82[EUR][1000 genomes]
rs17758420	0.83[EUR][1000 genomes]
rs17814023	0.83[EUR][1000 genomes]
rs17814065	0.96[CEU][hapmap];0.82[CHB][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs17814503	0.83[EUR][1000 genomes]
rs17814598	0.83[EUR][1000 genomes]
rs1812385	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1864371	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1865531	0.96[CEU][hapmap];0.82[CHB][hapmap];0.80[AMR][1000 genomes]
rs2007366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2068009	0.83[EUR][1000 genomes]
rs2115796	0.83[EUR][1000 genomes]
rs2115797	0.83[EUR][1000 genomes]
rs2163171	0.83[EUR][1000 genomes]
rs28393640	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3733461	0.88[CEU][hapmap]
rs3756081	0.91[CEU][hapmap];0.82[CHB][hapmap]
rs3756082	0.83[EUR][1000 genomes]
rs3756083	0.80[AMR][1000 genomes]
rs3775498	0.96[CEU][hapmap];0.82[CHB][hapmap];0.88[MEX][hapmap]
rs3815967	0.96[CEU][hapmap];0.82[CHB][hapmap];0.83[MEX][hapmap]
rs3948408	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4549398	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835283	0.88[CEU][hapmap]
rs4835284	0.88[CEU][hapmap]
rs4835286	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55736910	0.83[EUR][1000 genomes]
rs56174047	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56279747	0.83[EUR][1000 genomes]
rs56289966	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56333123	0.83[EUR][1000 genomes]
rs62326764	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62326797	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62326804	0.83[EUR][1000 genomes]
rs62326848	0.83[EUR][1000 genomes]
rs6537399	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537400	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6813969	0.85[CEU][hapmap]
rs6815527	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs6816161	0.96[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs6820462	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs6821066	0.83[EUR][1000 genomes]
rs6821479	0.83[EUR][1000 genomes]
rs6824313	0.83[EUR][1000 genomes]
rs6832576	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838174	0.88[CEU][hapmap]
rs6838458	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6839123	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs6839141	0.83[EUR][1000 genomes]
rs6843421	0.85[CEU][hapmap]
rs6844381	0.83[EUR][1000 genomes]
rs6856647	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72727922	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7657269	0.84[EUR][1000 genomes]
rs7745	0.83[EUR][1000 genomes]
rs919482	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs919483	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs9308199	0.96[CEU][hapmap];0.82[CHB][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7695415	LSM6	cis	parietal	SCAN
rs7695415	RP11-6L6.2	cis	Artery Tibial	GTEx
rs7695415	RP11-6L6.2	cis	lung	GTEx
rs7695415	RP11-6L6.2	cis	Skin Sun Exposed Lower leg	GTEx
rs7695415	RP11-6L6.2	cis	Adipose Subcutaneous	GTEx
rs7695415	RP11-6L6.2	cis	Nerve Tibial	GTEx
rs7695415	LSM6	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147054600-147056600	Enhancers	Fetal Brain Male	brain
2	chr4:147055200-147056600	Enhancers	Fetal Brain Female	brain
3	chr4:147055200-147057400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr4:147055200-147057400	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr4:147055400-147056600	Enhancers	HMEC	breast
6	chr4:147055400-147056800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr4:147055600-147056600	Enhancers	Esophagus	oesophagus
8	chr4:147055600-147056800	Enhancers	Brain Germinal Matrix	brain
9	chr4:147055600-147057200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:147055800-147056400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr4:147055800-147056600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:147055800-147056600	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr4:147055800-147056600	Enhancers	Osteobl	bone
14	chr4:147055800-147057400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:147055800-147057400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:147055800-147057600	Enhancers	Fetal Muscle Leg	muscle
17	chr4:147055800-147058000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr4:147055800-147058400	Enhancers	Adipose Nuclei	Adipose
19	chr4:147056000-147056600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:147056000-147056600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:147056000-147056600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:147056000-147056600	Enhancers	Right Atrium	heart
23	chr4:147056000-147056800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr4:147056000-147057200	Enhancers	Brain Cingulate Gyrus	brain
25	chr4:147056200-147056600	Enhancers	Brain Anterior Caudate	brain
26	chr4:147056200-147057600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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