Variant report

Variant	rs2288002
Chromosome Location	chr16:72057282-72057283
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10048111	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10048144	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10400963	0.85[JPT][hapmap]
rs10492813	0.82[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap]
rs10492814	0.82[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap]
rs1050361	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs1050363	0.87[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap]
rs10852511	0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs11075924	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs11643192	0.80[JPT][hapmap]
rs12162087	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12325266	0.80[JPT][hapmap]
rs12443622	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12446480	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12449073	0.85[JPT][hapmap]
rs12917999	0.86[ASN][1000 genomes]
rs12924413	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs12930205	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12930702	0.91[ASN][1000 genomes]
rs12932845	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.81[ASN][1000 genomes]
rs16973716	0.90[JPT][hapmap]
rs2070937	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2070939	0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs2072141	0.82[CHB][hapmap]
rs2081222	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2081223	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2236765	0.83[ASN][1000 genomes]
rs2241411	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap]
rs2287998	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2287999	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2288000	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2288001	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2303285	0.85[CHD][hapmap];0.80[JPT][hapmap]
rs251033	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2550035	0.82[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap]
rs2550038	0.82[CHB][hapmap]
rs2550868	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2550869	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2550870	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2550876	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2878404	0.81[CHD][hapmap]
rs3764310	0.81[CHD][hapmap]
rs3764311	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs3764314	0.82[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap]
rs3812984	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs3812986	0.84[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs3844425	0.91[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs3852781	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs3852782	0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs3852784	0.81[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs3890860	0.87[ASN][1000 genomes]
rs3909541	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs4238964	0.85[JPT][hapmap]
rs4788458	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4788609	0.84[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs4788610	0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs56139130	0.85[ASN][1000 genomes]
rs6499557	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6499562	0.90[JPT][hapmap]
rs7185840	0.87[ASN][1000 genomes]
rs7188962	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7189115	0.85[ASN][1000 genomes]
rs7189591	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7190994	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7192848	0.80[JPT][hapmap]
rs7198936	0.82[GIH][hapmap]
rs7199261	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7200854	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7201225	0.80[JPT][hapmap]
rs7201643	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7201866	0.88[ASN][1000 genomes]
rs7202268	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7203426	0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7203821	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7350838	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7940	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs8044868	0.90[JPT][hapmap]
rs8052338	0.85[JPT][hapmap]
rs8052408	0.90[JPT][hapmap]
rs8053907	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8059437	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.82[ASN][1000 genomes]
rs8062895	0.81[CHD][hapmap]
rs8182213	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9924964	0.84[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs9926927	0.82[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap]
rs9927526	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs9928157	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs9932951	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.91[ASN][1000 genomes]
rs9936642	0.80[JPT][hapmap]
rs9938382	0.83[AMR][1000 genomes];0.91[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	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1055854	chr16:71922144-72082886	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv833273	chr16:71971805-72152854	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	esv2758430	chr16:71976344-72274347	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	esv2758654	chr16:71976344-72274347	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv428329	chr16:71976344-72274347	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	esv1843253	chr16:72042428-72059149	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2288002	NRN1L	cis	parietal	SCAN
rs2288002	DHODH	cis	cerebellum	SCAN
rs2288002	HP	cis	cerebellum	SCAN
rs2288002	HP	cis	parietal	SCAN
rs2288002	HPR	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72043000-72063000	Weak transcription	Small Intestine	intestine
2	chr16:72043200-72057400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr16:72043200-72057800	Weak transcription	NHDF-Ad	bronchial
4	chr16:72043200-72061200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr16:72043200-72062800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr16:72043200-72069800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr16:72043200-72069800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr16:72043600-72075200	Weak transcription	Fetal Brain Male	brain
9	chr16:72044000-72057400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr16:72045600-72059400	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr16:72045600-72060200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr16:72045600-72060400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr16:72045600-72060600	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr16:72045600-72062200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr16:72045600-72062400	Strong transcription	Dnd41	blood
16	chr16:72045800-72060200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr16:72045800-72060400	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr16:72045800-72060400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr16:72045800-72064200	Strong transcription	Fetal Stomach	stomach
20	chr16:72046000-72060200	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr16:72046000-72064000	Strong transcription	Primary T cells from cord blood	blood
22	chr16:72046400-72060200	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr16:72046400-72062200	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr16:72047400-72059000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr16:72047800-72062000	Strong transcription	Thymus	Thymus
26	chr16:72047800-72062200	Strong transcription	Stomach Smooth Muscle	stomach
27	chr16:72048000-72057400	Weak transcription	Colonic Mucosa	Colon
28	chr16:72048000-72058600	Strong transcription	Primary B cells from peripheral blood	blood
29	chr16:72048000-72060400	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr16:72048000-72063000	Weak transcription	NH-A	brain
31	chr16:72048200-72060400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr16:72048600-72059800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr16:72048600-72060200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr16:72048600-72063800	Strong transcription	Fetal Muscle Trunk	muscle
35	chr16:72048800-72060600	Weak transcription	Fetal Heart	heart
36	chr16:72049000-72060200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr16:72049200-72062000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr16:72049600-72062600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr16:72050600-72062600	Strong transcription	Fetal Muscle Leg	muscle
40	chr16:72051000-72062600	Strong transcription	Left Ventricle	heart
41	chr16:72051200-72060200	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr16:72051400-72061000	Weak transcription	HMEC	breast
43	chr16:72051400-72063800	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr16:72051400-72078600	Weak transcription	Fetal Kidney	kidney
45	chr16:72051600-72057800	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr16:72051600-72057800	Weak transcription	K562	blood
47	chr16:72052600-72060200	Strong transcription	Adipose Nuclei	Adipose
48	chr16:72052800-72065200	Genic enhancers	Liver	Liver
49	chr16:72053000-72058600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr16:72053600-72057600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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