Variant report

Variant	rs4889614
Chromosome Location	chr16:30862135-30862136
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:30860781..30863183-chr16:30905990..30907555,2	MCF-7	breast:
2	chr16:30860522..30863140-chr2:219958844..219961446,2	K562	blood:
3	chr16:30850477..30852478-chr16:30860687..30863396,2	K562	blood:
4	chr16:30860894..30863329-chr16:30866893..30870535,3	K562	blood:
5	chr16:30859440..30862279-chr16:30910086..30912107,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000262721	Chromatin interaction
ENSG00000099385	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11150596	0.82[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11150599	0.82[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs11647697	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11862962	0.84[ASN][1000 genomes]
rs11864054	0.81[ASN][1000 genomes]
rs12920259	0.87[ASN][1000 genomes]
rs12926237	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12926295	0.82[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs12928081	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12929065	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12930944	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13338946	0.93[GIH][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap]
rs1458201	0.84[CEU][hapmap]
rs2125293	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2168834	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2289442	0.93[GIH][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap]
rs2335013	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2878304	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34840035	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35629860	0.93[GIH][hapmap];0.86[JPT][hapmap];0.92[TSI][hapmap]
rs35675346	0.84[CEU][hapmap]
rs3747481	0.92[GIH][hapmap];0.85[TSI][hapmap]
rs3747486	0.90[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs3812999	0.93[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs4290486	0.87[ASN][1000 genomes]
rs4889490	0.86[JPT][hapmap]
rs4889534	1.00[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4889536	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4889622	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4889627	0.94[ASN][1000 genomes]
rs4889630	1.00[ASW][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4889631	0.86[AFR][1000 genomes]
rs4889651	0.81[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4889653	0.81[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55719146	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56083427	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67264578	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67456613	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7187359	0.93[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs7198250	0.93[GIH][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap]
rs7200879	0.84[CEU][hapmap]
rs72799330	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7500719	0.82[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.81[ASN][1000 genomes]
rs8046001	0.82[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs8046391	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs8050107	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8058578	0.93[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs8058961	0.97[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs8059475	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8063565	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs885107	0.90[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs897984	0.87[ASN][1000 genomes]
rs9796842	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9932572	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9933843	0.82[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv1064134	chr16:30640293-31087327	Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	238 gene(s)	inside rSNPs	diseases
4	nsv905728	chr16:30642867-30928970	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	171 gene(s)	inside rSNPs	diseases
5	nsv905729	chr16:30642867-31247924	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
6	esv1825223	chr16:30669091-30971810	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
7	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
8	nsv905733	chr16:30796919-31004812	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
9	nsv869652	chr16:30799471-30951038	Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
10	nsv1060384	chr16:30802415-30878838	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
11	nsv1059633	chr16:30803099-30867916	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	nsv833189	chr16:30819708-30960795	Active TSS Weak transcription Strong transcription Enhancers Flanking 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	79 gene(s)	inside rSNPs	diseases
13	nsv833190	chr16:30845051-31007863	Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	105 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4889614	ITGAX	cis	parietal	SCAN
rs4889614	MYST1	cis	cerebellum	SCAN
rs4889614	MYST1	cis	parietal	SCAN
rs4889614	NNT	trans	cerebellum	SCAN
rs4889614	GCFC1	trans	cerebellum	SCAN
rs4889614	C16orf93	cis	parietal	SCAN
rs4889614	PHKG2	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30845800-30884800	Weak transcription	Brain Germinal Matrix	brain
2	chr16:30846200-30863000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr16:30846400-30883400	Weak transcription	Fetal Brain Female	brain
4	chr16:30846800-30885600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr16:30856200-30885800	Weak transcription	NH-A	brain
6	chr16:30856400-30883400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr16:30856600-30863200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr16:30856600-30864800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr16:30856600-30865200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr16:30856600-30867800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr16:30856600-30869200	Weak transcription	HSMM	muscle
12	chr16:30856600-30883400	Weak transcription	Lung	lung
13	chr16:30856600-30885000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr16:30856800-30862600	Weak transcription	Fetal Stomach	stomach
15	chr16:30856800-30862800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr16:30856800-30863000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr16:30856800-30864600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr16:30856800-30864600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr16:30856800-30864600	Weak transcription	Primary B cells from cord blood	blood
20	chr16:30856800-30864600	Weak transcription	Fetal Kidney	kidney
21	chr16:30856800-30864600	Weak transcription	Fetal Lung	lung
22	chr16:30856800-30865000	Weak transcription	Fetal Intestine Large	intestine
23	chr16:30856800-30865200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr16:30856800-30865200	Weak transcription	Brain Anterior Caudate	brain
25	chr16:30856800-30869600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr16:30856800-30871200	Weak transcription	Aorta	Aorta
27	chr16:30856800-30882400	Weak transcription	Brain Substantia Nigra	brain
28	chr16:30856800-30883400	Weak transcription	Pancreas	Pancrea
29	chr16:30856800-30883600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr16:30856800-30883600	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr16:30856800-30883600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr16:30856800-30885600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr16:30856800-30885600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr16:30856800-30885600	Weak transcription	Esophagus	oesophagus
35	chr16:30856800-30885600	Weak transcription	Spleen	Spleen
36	chr16:30856800-30885800	Weak transcription	Brain Angular Gyrus	brain
37	chr16:30857000-30862400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr16:30857000-30864600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr16:30857000-30864800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr16:30857000-30864800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr16:30857000-30864800	Weak transcription	Adipose Nuclei	Adipose
42	chr16:30857000-30864800	Weak transcription	Colon Smooth Muscle	Colon
43	chr16:30857000-30865200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr16:30857000-30866000	Weak transcription	Fetal Intestine Small	intestine
45	chr16:30857000-30867800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr16:30857000-30868000	Weak transcription	HepG2	liver
47	chr16:30857000-30868200	Weak transcription	Primary T cells from cord blood	blood
48	chr16:30857000-30868200	Weak transcription	Right Ventricle	heart
49	chr16:30857000-30869600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr16:30857000-30883200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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