Variant report

Variant	rs4709709
Chromosome Location	chr6:163761626-163761627
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:163721882..163723526-chr6:163759692..163762187,2	K562	blood:
2	chr6:163760779..163762699-chr6:163768493..163770120,2	K562	blood:
3	chr6:163755571..163762023-chr6:163831891..163837157,6	MCF-7	breast:
4	chr6:163759847..163762654-chr6:163834528..163837162,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AL078585.1-2	chr6:163761441-163762062	XLOC_005909

Variant related genes	Relation type
ENSG00000112531	Chromatin interaction
ENSG00000270419	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10945892	0.80[AMR][1000 genomes]
rs11759068	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11964527	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12662804	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12664344	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3734284	0.83[CEU][hapmap];0.89[CHB][hapmap];0.86[EUR][1000 genomes]
rs4709704	0.88[CEU][hapmap];0.83[CHB][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4709705	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4709706	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709708	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56654356	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62428053	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62430070	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62430071	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62430072	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62430073	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62430074	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932137	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs6932471	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs742331	0.90[CHB][hapmap]
rs882246	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1022610	chr6:163591786-163814041	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv605188	chr6:163697439-163772096	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv534621	chr6:163731741-163950870	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163745200-163767000	Enhancers	Brain Inferior Temporal Lobe	brain
2	chr6:163745600-163773600	Enhancers	Brain Substantia Nigra	brain
3	chr6:163746600-163764400	Enhancers	Brain Cingulate Gyrus	brain
4	chr6:163756800-163764800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:163757400-163762400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:163758000-163764200	Weak transcription	Spleen	Spleen
7	chr6:163758800-163762600	Enhancers	HSMMtube	muscle
8	chr6:163759000-163768400	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr6:163759200-163765200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:163759400-163762000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:163759600-163763000	Enhancers	HSMM	muscle
12	chr6:163760200-163762400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:163760200-163762400	Weak transcription	Left Ventricle	heart
14	chr6:163760200-163762400	Weak transcription	Psoas Muscle	Psoas
15	chr6:163760200-163762400	Weak transcription	Right Ventricle	heart
16	chr6:163760200-163762600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:163760200-163762600	Weak transcription	Placenta	Placenta
18	chr6:163760200-163762600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr6:163760200-163763200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:163760200-163763800	Enhancers	Brain Angular Gyrus	brain
21	chr6:163760200-163764200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:163760200-163767000	Weak transcription	Esophagus	oesophagus
23	chr6:163760400-163761800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr6:163760400-163762400	Weak transcription	Adipose Nuclei	Adipose
25	chr6:163760400-163762400	Weak transcription	Right Atrium	heart
26	chr6:163760400-163763800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:163760600-163762400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr6:163760600-163762600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr6:163760600-163762600	Enhancers	Fetal Heart	heart
30	chr6:163760600-163763000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr6:163760800-163761800	Weak transcription	Fetal Muscle Leg	muscle
32	chr6:163760800-163762000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:163760800-163762200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:163760800-163762400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:163760800-163762600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr6:163760800-163763400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:163760800-163764000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr6:163760800-163765200	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr6:163760800-163767200	Enhancers	Brain Hippocampus Middle	brain
40	chr6:163760800-163767400	Weak transcription	NH-A	brain
41	chr6:163761200-163762000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr6:163761400-163767000	Weak transcription	Brain Germinal Matrix	brain
43	chr6:163761400-163767200	Enhancers	Brain Anterior Caudate	brain

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