Variant report

Variant	rs6499560
Chromosome Location	chr16:72147666-72147667
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1035559	0.84[CEU][hapmap];0.89[GIH][hapmap]
rs10400963	0.88[YRI][hapmap]
rs10492813	0.84[CEU][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10492814	0.84[CEU][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1050361	0.87[CEU][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1050362	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1050363	0.90[JPT][hapmap];0.81[YRI][hapmap]
rs11075922	0.84[ASN][1000 genomes]
rs11862813	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11864453	0.84[CEU][hapmap];0.89[GIH][hapmap]
rs12325142	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12444701	0.92[ASN][1000 genomes]
rs12445401	0.92[ASN][1000 genomes]
rs12445586	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12448315	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12449073	0.87[YRI][hapmap]
rs12708925	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12708926	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12708927	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12708928	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12924413	0.95[JPT][hapmap];0.81[YRI][hapmap]
rs12924886	0.83[ASN][1000 genomes]
rs12928732	0.90[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs12932845	0.81[YRI][hapmap]
rs12933838	0.82[ASN][1000 genomes]
rs13334151	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs16973716	0.85[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs2000999	0.84[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2072141	0.82[CEU][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap]
rs2072142	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2074626	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2074627	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs217181	0.81[YRI][hapmap]
rs2240243	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2241411	0.81[JPT][hapmap]
rs2241412	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2269918	0.82[AMR][1000 genomes]
rs2287997	0.97[ASN][1000 genomes]
rs2303285	0.84[CEU][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes]
rs2550035	0.84[CEU][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap]
rs2550038	0.84[CEU][hapmap];0.89[JPT][hapmap]
rs28432692	0.82[ASN][1000 genomes]
rs2854956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34042070	0.85[ASN][1000 genomes]
rs34714490	0.83[ASN][1000 genomes]
rs35460163	0.83[ASN][1000 genomes]
rs3764311	0.84[CEU][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3764312	0.81[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3764314	0.84[CEU][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3794695	0.86[ASN][1000 genomes]
rs3812987	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3844425	0.81[YRI][hapmap]
rs3852781	0.84[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3852782	0.87[YRI][hapmap]
rs3852784	0.87[YRI][hapmap]
rs3902135	0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs3909542	0.81[AFR][1000 genomes]
rs4238964	0.90[LWK][hapmap];0.94[YRI][hapmap]
rs4788609	0.87[YRI][hapmap]
rs4788610	0.81[YRI][hapmap]
rs5472	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6416742	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6499559	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6499561	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6499562	0.85[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs6680	0.88[ASW][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7184169	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7185407	0.84[CEU][hapmap];0.89[GIH][hapmap]
rs7188058	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7190995	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7191127	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7192730	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7197453	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7197869	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7198572	0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7940	0.81[JPT][hapmap];0.81[YRI][hapmap]
rs8043606	0.80[ASN][1000 genomes]
rs8044555	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8044868	0.85[CHB][hapmap];0.85[JPT][hapmap];0.90[LWK][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs8047377	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8050238	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8051882	0.88[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8052408	0.85[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs8058609	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8059378	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8059437	0.81[JPT][hapmap];0.81[YRI][hapmap]
rs8061282	0.92[ASN][1000 genomes]
rs8061459	0.92[ASN][1000 genomes]
rs8062041	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9302635	0.82[ASW][hapmap];0.97[LWK][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes]
rs9925763	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9926156	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9926927	0.84[CEU][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9927526	0.87[YRI][hapmap]
rs9928157	0.81[JPT][hapmap];0.86[YRI][hapmap]
rs9932062	0.80[ASN][1000 genomes]
rs9932951	0.81[JPT][hapmap];0.87[YRI][hapmap]
rs9941087	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9941346	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
3	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
4	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
5	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
6	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
7	nsv534588	chr16:72078262-72287230	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6499560	HPR	cis	cerebellum	SCAN
rs6499560	DHX38	cis	multi-tissue	Pritchard
rs6499560	DHX38	cis	lymphoblastoid	seeQTL
rs6499560	HP	cis	cerebellum	SCAN
rs6499560	DHODH	cis	cerebellum	SCAN
rs6499560	HP	cis	parietal	SCAN
rs6499560	DHODH	cis	Artery Tibial	GTEx
rs6499560	NRN1L	cis	parietal	SCAN
rs6499560	DHX38	cis	brain	BrainEAC
rs6499560	DHODH	cis	Nerve Tibial	GTEx
rs6499560	HPR	cis	parietal	SCAN
rs6499560	HP	cis	multi-tissue	Pritchard
rs6499560	DHX38	cis	Lymphoblastoid	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72129400-72147800	Strong transcription	Primary T cells from cord blood	blood
2	chr16:72129800-72147800	Strong transcription	Sigmoid Colon	Sigmoid Colon
3	chr16:72129800-72148200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr16:72129800-72149000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr16:72130000-72147800	Strong transcription	Primary T helper cells PMA-I stimulated	--
6	chr16:72130000-72147800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr16:72130000-72147800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr16:72130000-72147800	Strong transcription	Brain Anterior Caudate	brain
9	chr16:72130000-72147800	Strong transcription	Brain Hippocampus Middle	brain
10	chr16:72130000-72147800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr16:72130000-72147800	Strong transcription	Fetal Stomach	stomach
12	chr16:72130000-72147800	Strong transcription	Thymus	Thymus
13	chr16:72130000-72147800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr16:72130000-72148000	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr16:72130000-72148000	Strong transcription	Brain Cingulate Gyrus	brain
16	chr16:72130000-72148200	Strong transcription	Liver	Liver
17	chr16:72130000-72148200	Strong transcription	Placenta	Placenta
18	chr16:72130200-72147800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr16:72130200-72147800	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr16:72130200-72148000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr16:72130800-72148000	Strong transcription	Brain Germinal Matrix	brain
22	chr16:72134600-72147800	Strong transcription	Fetal Muscle Trunk	muscle
23	chr16:72135600-72148400	Strong transcription	Fetal Muscle Leg	muscle
24	chr16:72136200-72148200	Strong transcription	Primary B cells from cord blood	blood
25	chr16:72136400-72148600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr16:72142800-72158600	Weak transcription	Fetal Brain Male	brain
27	chr16:72143000-72152200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr16:72145600-72147800	Strong transcription	Fetal Intestine Small	intestine
29	chr16:72145800-72150000	Weak transcription	K562	blood
30	chr16:72145800-72150200	Weak transcription	Osteobl	bone
31	chr16:72145800-72152600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr16:72145800-72156000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr16:72145800-72160400	Weak transcription	HMEC	breast
34	chr16:72146000-72147800	Weak transcription	HSMMtube	muscle
35	chr16:72146200-72147800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr16:72146200-72147800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr16:72146200-72148200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr16:72146400-72148400	Weak transcription	HSMM	muscle
39	chr16:72146400-72148800	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr16:72146400-72158600	Weak transcription	Colon Smooth Muscle	Colon
41	chr16:72146400-72159000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr16:72146600-72148200	Weak transcription	Psoas Muscle	Psoas
43	chr16:72146600-72148200	Weak transcription	Small Intestine	intestine
44	chr16:72146600-72152800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr16:72146600-72154600	Weak transcription	HUVEC	blood vessel
46	chr16:72146600-72155000	Weak transcription	Stomach Mucosa	stomach
47	chr16:72146600-72159000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr16:72146600-72159200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr16:72146600-72166600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr16:72146800-72148600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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