Variant report

Variant	rs17079835
Chromosome Location	chr6:150858993-150858994
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:150858643..150861809-chr6:150864654..150868383,3	K562	blood:
2	chr6:150856840..150859421-chr6:151018731..151021434,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10499263	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10499264	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13193322	0.83[AFR][1000 genomes]
rs13196518	0.83[AFR][1000 genomes]
rs13197203	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13199757	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13206793	0.83[AFR][1000 genomes]
rs13217733	0.80[EUR][1000 genomes]
rs13218019	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17079805	0.83[AFR][1000 genomes]
rs17079846	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17079852	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17079861	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs33951563	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34120777	0.80[EUR][1000 genomes]
rs34393000	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34537150	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34597508	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34713924	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34779574	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34782866	0.81[AFR][1000 genomes]
rs35046394	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35260192	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4323319	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.84[MEX][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4566894	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs55708277	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs59435275	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs67925488	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6924786	0.83[AFR][1000 genomes]
rs7774671	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9688466	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[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	nsv1020067	chr6:150730783-150870708	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv886772	chr6:150743364-151024280	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv464079	chr6:150836676-150873766	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv604850	chr6:150836676-150873766	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17079835	PCMT1	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150857000-150862400	Weak transcription	Fetal Lung	lung
2	chr6:150857600-150859000	Enhancers	Fetal Muscle Trunk	muscle
3	chr6:150857600-150860200	Weak transcription	Liver	Liver
4	chr6:150857600-150862400	Weak transcription	HepG2	liver
5	chr6:150858000-150859200	Enhancers	Brain Substantia Nigra	brain
6	chr6:150858000-150859200	Enhancers	Fetal Muscle Leg	muscle
7	chr6:150858000-150859400	Enhancers	Brain Hippocampus Middle	brain
8	chr6:150858000-150860200	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr6:150858000-150864000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:150858000-150864200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:150858200-150859200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:150858200-150859400	Enhancers	Brain Cingulate Gyrus	brain
13	chr6:150858200-150860000	Enhancers	Stomach Smooth Muscle	stomach
14	chr6:150858400-150859000	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr6:150858400-150859400	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr6:150858400-150859400	Enhancers	Colon Smooth Muscle	Colon
17	chr6:150858400-150859400	Enhancers	Rectal Smooth Muscle	rectum
18	chr6:150858400-150859600	Enhancers	Adipose Nuclei	Adipose
19	chr6:150858600-150859200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:150858600-150860000	Enhancers	Left Ventricle	heart
21	chr6:150858800-150859000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:150858800-150859000	Enhancers	Right Atrium	heart
23	chr6:150858800-150859000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr6:150858800-150859800	Enhancers	Brain Anterior Caudate	brain
25	chr6:150858800-150859800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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