Variant report

Variant	rs16859787
Chromosome Location	chr3:112274613-112274614
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:112270877..112274678-chr3:112278992..112281610,4	MCF-7	breast:
2	chr3:112272044..112274714-chr3:112358450..112360286,2	MCF-7	breast:
3	chr3:112267834..112269856-chr3:112273355..112275580,2	MCF-7	breast:
4	chr3:112272255..112274870-chr3:112277581..112280165,3	K562	blood:
5	chr3:112274013..112276880-chr3:112736926..112739647,2	MCF-7	breast:
6	chr3:112273986..112276332-chr3:112279376..112281873,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240057	Chromatin interaction
ENSG00000144848	Chromatin interaction
ENSG00000091986	Chromatin interaction
ENSG00000138459	Chromatin interaction
ENSG00000163608	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10511317	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11919639	1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11921669	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13059364	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13063173	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13064534	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13065703	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13070342	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13071492	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13080547	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13080749	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13081201	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13081265	0.89[EUR][1000 genomes]
rs13081632	0.89[EUR][1000 genomes]
rs13088339	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13088349	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13088467	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13092057	0.81[ASN][1000 genomes]
rs13094161	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13094649	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13095000	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs13096943	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16845067	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16859629	0.86[JPT][hapmap]
rs16859632	0.86[JPT][hapmap]
rs16859661	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16859674	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs16859727	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16859758	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16859775	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16859779	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16859793	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1994711	1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap]
rs2220656	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2705526	0.85[EUR][1000 genomes]
rs28365853	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2942062	1.00[JPT][hapmap];0.85[TSI][hapmap]
rs34080815	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34139211	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34248586	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34284082	0.96[EUR][1000 genomes]
rs34541731	1.00[EUR][1000 genomes]
rs34596334	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs34597203	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34645913	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34829517	1.00[EUR][1000 genomes]
rs34889961	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34949685	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34962178	1.00[EUR][1000 genomes]
rs35107041	0.82[EUR][1000 genomes]
rs35240469	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35255669	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35349986	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35512450	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35526995	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35529363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35692417	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35709173	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35725070	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35748518	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35803911	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35840933	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35931975	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs36025914	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36031379	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36045008	1.00[EUR][1000 genomes]
rs36061184	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36146261	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36153507	1.00[EUR][1000 genomes]
rs3736269	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3736270	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3736271	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3773698	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3773701	1.00[EUR][1000 genomes]
rs3773704	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3773706	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3773710	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821684	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55742760	1.00[EUR][1000 genomes]
rs56662636	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56856838	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56970524	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57346109	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58891772	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59279185	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59305071	0.94[AFR][1000 genomes]
rs59858117	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60321074	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60646325	1.00[EUR][1000 genomes]
rs66486470	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66698345	0.96[EUR][1000 genomes]
rs66791711	1.00[EUR][1000 genomes]
rs66910014	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67021100	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67204151	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs67513863	0.96[EUR][1000 genomes]
rs67940544	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67944354	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71317505	0.85[EUR][1000 genomes]
rs71317506	0.89[EUR][1000 genomes]
rs71317507	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71317508	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71317510	1.00[EUR][1000 genomes]
rs724125	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73229350	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73229353	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73229398	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs958935	1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003936	chr3:112125931-112274613	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv998309	chr3:112130290-112278804	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1006065	chr3:112147080-112276983	Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1005323	chr3:112171990-112274613	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv591301	chr3:112252532-112332629	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16859787	SLC35A5	cis	multi-tissue	Pritchard
rs16859787	SLC35A5	cis	Nerve Tibial	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112244400-112278200	Weak transcription	K562	blood
2	chr3:112244400-112278400	Weak transcription	HSMMtube	muscle
3	chr3:112245800-112279600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:112247600-112279600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:112249200-112275800	Weak transcription	Fetal Stomach	stomach
6	chr3:112249200-112276000	Weak transcription	Spleen	Spleen
7	chr3:112249200-112278200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:112249200-112278400	Weak transcription	Aorta	Aorta
9	chr3:112249200-112279600	Weak transcription	Esophagus	oesophagus
10	chr3:112249200-112279600	Weak transcription	Gastric	stomach
11	chr3:112249200-112279800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:112249400-112276200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:112249400-112279600	Weak transcription	Lung	lung
14	chr3:112252600-112278400	Weak transcription	Fetal Kidney	kidney
15	chr3:112253200-112278600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr3:112260000-112278200	Weak transcription	Fetal Brain Male	brain
17	chr3:112260400-112279600	Weak transcription	Pancreas	Pancrea
18	chr3:112265000-112276000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:112266200-112278200	Weak transcription	Fetal Heart	heart
20	chr3:112266200-112278200	Weak transcription	NHLF	lung
21	chr3:112266200-112278400	Weak transcription	Colonic Mucosa	Colon
22	chr3:112266400-112278200	Weak transcription	NHEK	skin
23	chr3:112266800-112278400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:112267000-112278400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr3:112267000-112278400	Weak transcription	NHDF-Ad	bronchial
26	chr3:112267200-112276000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:112267200-112276000	Weak transcription	Fetal Muscle Leg	muscle
28	chr3:112267200-112278400	Weak transcription	Thymus	Thymus
29	chr3:112267200-112279200	Weak transcription	Right Ventricle	heart
30	chr3:112267600-112274800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:112267600-112275800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr3:112267600-112278200	Weak transcription	Ovary	ovary
33	chr3:112267600-112278600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr3:112267600-112279600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr3:112267800-112275800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:112267800-112276000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr3:112267800-112278200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:112267800-112278200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:112267800-112278200	Weak transcription	Fetal Brain Female	brain
40	chr3:112267800-112278400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:112267800-112278400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr3:112267800-112278400	Weak transcription	NH-A	brain
43	chr3:112268000-112276000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:112268000-112278200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:112268000-112278200	Weak transcription	Duodenum Mucosa	Duodenum
46	chr3:112268000-112278200	Weak transcription	Fetal Lung	lung
47	chr3:112268000-112278200	Weak transcription	Osteobl	bone
48	chr3:112268200-112275800	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr3:112268200-112278000	Weak transcription	Brain Germinal Matrix	brain
50	chr3:112268600-112278400	Weak transcription	Placenta	Placenta

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