Variant report

Variant	rs16832604
Chromosome Location	chr1:150957730-150957731
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150955685..150958316-chr1:150971116..150974033,3	MCF-7	breast:
2	chr1:150949558..150951518-chr1:150957213..150958786,2	K562	blood:
3	chr1:150955747..150957979-chr1:150977182..150980115,2	K562	blood:
4	chr1:150952248..150956266-chr1:150957653..150962515,6	K562	blood:
5	chr1:150952182..150958148-chr1:150976816..150982947,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143412	Chromatin interaction
ENSG00000143409	Chromatin interaction
ENSG00000143363	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10157132	0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs11204727	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs11579289	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12040707	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12042263	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12044969	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12097548	0.91[AFR][1000 genomes]
rs16827772	0.88[YRI][hapmap]
rs16832391	0.88[YRI][hapmap];0.86[AFR][1000 genomes]
rs2134688	0.84[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2305812	0.92[CHB][hapmap];0.92[ASN][1000 genomes]
rs2305815	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs267736	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34090972	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3738483	0.84[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs3754210	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820541	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs4379678	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs533928	0.87[ASN][1000 genomes]
rs539118	0.96[ASN][1000 genomes]
rs55884154	0.84[AFR][1000 genomes]
rs57378704	0.87[AFR][1000 genomes]
rs57734108	0.92[AFR][1000 genomes]
rs57746902	0.95[AFR][1000 genomes]
rs58338969	0.87[AFR][1000 genomes]
rs61817649	0.89[ASN][1000 genomes]
rs6671489	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6672625	0.95[AFR][1000 genomes]
rs6679701	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs6688248	0.89[ASN][1000 genomes]
rs72706512	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74127089	0.87[AFR][1000 genomes]
rs74127091	0.87[AFR][1000 genomes]
rs74127092	0.83[AFR][1000 genomes]
rs74128604	0.89[AFR][1000 genomes]
rs74128609	0.93[AFR][1000 genomes]
rs7517566	0.84[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs7521445	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7522741	0.87[AFR][1000 genomes]
rs7535032	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7535848	0.89[ASN][1000 genomes]
rs7547614	0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs771203	0.96[ASN][1000 genomes]
rs771204	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs771205	0.92[CHB][hapmap];0.95[ASN][1000 genomes]
rs9988459	0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv1008496	chr1:150845827-150970656	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	nsv522317	chr1:150933723-150974162	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16832604	ADAMTSL4,LOC100289061	cis	brain	BrainEAC

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150952000-150968000	Weak transcription	Spleen	Spleen
2	chr1:150952600-150957800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:150952600-150960800	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr1:150952600-150968000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:150953600-150959000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:150954200-150969400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:150954600-150957800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:150954800-150968000	Weak transcription	Fetal Kidney	kidney
9	chr1:150955000-150969400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:150955400-150957800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:150955400-150957800	Weak transcription	A549	lung
12	chr1:150955400-150969400	Weak transcription	Gastric	stomach
13	chr1:150955400-150970400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:150955400-150978800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:150955600-150967600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:150955600-150968200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:150955800-150967600	Weak transcription	Fetal Intestine Small	intestine
18	chr1:150956200-150958600	Weak transcription	Liver	Liver
19	chr1:150956200-150969400	Weak transcription	Fetal Intestine Large	intestine
20	chr1:150956600-150958200	Enhancers	Pancreas	Pancrea
21	chr1:150957200-150957800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:150957400-150958000	Enhancers	HepG2	liver
23	chr1:150957400-150958000	Enhancers	K562	blood
24	chr1:150957400-150958400	Enhancers	Hela-S3	cervix
25	chr1:150957600-150957800	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr1:150957600-150958000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:150957600-150958200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:150957600-150958400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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