Variant report

Variant	rs4889658
Chromosome Location	chr16:31450817-31450818
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:31438431..31440952-chr16:31448443..31451186,2	MCF-7	breast:
2	chr16:31446244..31450994-chr16:31452849..31455131,6	K562	blood:
3	chr16:31440314..31442946-chr16:31447999..31450957,2	K562	blood:
4	chr16:31444237..31446824-chr16:31447860..31450827,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176723	Chromatin interaction
ENSG00000156885	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2472050	0.88[MEX][hapmap]
rs4889659	0.93[YRI][hapmap];0.89[AFR][1000 genomes]
rs60239608	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62051544	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66989296	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7202020	0.84[JPT][hapmap]
rs8045738	0.89[ASW][hapmap];0.81[CEU][hapmap];0.85[GIH][hapmap];0.95[LWK][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059459	chr16:31299088-31462251	Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv542901	chr16:31299088-31462251	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv3392534	chr16:31303038-31573066	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
4	nsv833194	chr16:31358179-31528545	Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
5	nsv905747	chr16:31394179-31888684	Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	123 gene(s)	inside rSNPs	diseases
6	nsv1066280	chr16:31396464-31452067	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv905748	chr16:31427678-31559220	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
8	nsv905749	chr16:31427678-31565597	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	96 gene(s)	inside rSNPs	diseases
9	nsv905750	chr16:31427678-31587662	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	98 gene(s)	inside rSNPs	diseases
10	nsv905751	chr16:31431360-31489033	Bivalent Enhancer Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
11	nsv905752	chr16:31436932-31565597	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	95 gene(s)	inside rSNPs	diseases
12	nsv905753	chr16:31436932-31587662	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4889658	CD19	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31439600-31453200	Weak transcription	Lung	lung
2	chr16:31439600-31453800	Weak transcription	Gastric	stomach
3	chr16:31439600-31454000	Weak transcription	Aorta	Aorta
4	chr16:31439800-31451600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr16:31439800-31453200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr16:31439800-31453400	Weak transcription	Fetal Brain Female	brain
7	chr16:31440400-31453200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr16:31440600-31451800	Weak transcription	Brain Hippocampus Middle	brain
9	chr16:31440600-31453200	Weak transcription	Liver	Liver
10	chr16:31441000-31453200	Weak transcription	Brain Anterior Caudate	brain
11	chr16:31442200-31453800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr16:31445400-31453400	Weak transcription	Left Ventricle	heart
13	chr16:31445400-31453400	Weak transcription	Psoas Muscle	Psoas
14	chr16:31445600-31452400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr16:31448000-31453000	Weak transcription	Ovary	ovary
16	chr16:31448000-31454000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr16:31448200-31453000	Weak transcription	Pancreas	Pancrea
18	chr16:31448200-31453200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr16:31448200-31453200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr16:31448200-31453200	Weak transcription	Fetal Stomach	stomach
21	chr16:31448200-31453200	Weak transcription	Spleen	Spleen
22	chr16:31448200-31453400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr16:31448400-31453200	Weak transcription	Fetal Intestine Large	intestine
24	chr16:31448400-31453400	Weak transcription	Fetal Intestine Small	intestine
25	chr16:31448400-31453400	Weak transcription	Right Ventricle	heart
26	chr16:31449800-31451200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr16:31449800-31451200	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr16:31449800-31451400	Enhancers	GM12878-XiMat	blood
29	chr16:31450000-31451200	Enhancers	Primary B cells from cord blood	blood
30	chr16:31450000-31451200	Enhancers	Primary B cells from peripheral blood	blood
31	chr16:31450200-31454000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr16:31450600-31452000	Weak transcription	Fetal Muscle Leg	muscle
33	chr16:31450800-31451000	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr16:31450800-31453400	Enhancers	Skeletal Muscle Male	skeletal muscle

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