Variant report

Variant	rs7200854
Chromosome Location	chr16:72083318-72083319
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 131 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10048111	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10048144	0.82[AMR][1000 genomes]
rs10400963	0.90[JPT][hapmap]
rs10492813	0.86[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs10492814	0.86[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs1050361	0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1050362	0.81[JPT][hapmap]
rs1050363	0.91[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs10852511	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs11075924	0.91[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap]
rs11643192	0.85[JPT][hapmap]
rs11862813	0.80[ASN][1000 genomes]
rs12162087	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12325142	0.81[JPT][hapmap]
rs12325266	0.85[JPT][hapmap]
rs12443622	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12446480	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12449073	0.90[JPT][hapmap]
rs12708925	0.81[ASN][1000 genomes]
rs12708928	0.81[JPT][hapmap]
rs12917999	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12924413	0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs12930205	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12930702	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12932845	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12935266	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs16973716	0.81[GIH][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs2070937	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2070939	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2072141	0.86[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs2072142	0.81[JPT][hapmap]
rs2074626	0.85[JPT][hapmap]
rs2074627	0.81[JPT][hapmap]
rs2081222	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2081223	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2236765	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2240243	0.81[JPT][hapmap]
rs2241411	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2241412	0.81[JPT][hapmap]
rs2287998	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2287999	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2288000	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2288001	0.90[ASN][1000 genomes]
rs2288002	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2303285	0.82[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs251033	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2550035	0.86[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2550038	0.86[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2550868	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2550869	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2550870	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2550876	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2854956	0.81[JPT][hapmap];0.87[YRI][hapmap]
rs2878404	0.81[CHD][hapmap]
rs3764310	0.81[CHD][hapmap]
rs3764311	0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs3764314	0.86[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs3812984	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs3812986	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs3812987	0.81[JPT][hapmap]
rs3844425	0.81[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs3852781	0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs3852782	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs3852784	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs3890860	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3909541	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs3909542	0.87[EUR][1000 genomes]
rs4238964	0.90[JPT][hapmap]
rs4788458	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4788461	0.83[EUR][1000 genomes]
rs4788598	0.92[YRI][hapmap]
rs4788609	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs4788610	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs56139130	0.92[ASN][1000 genomes]
rs6499557	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499562	0.81[GIH][hapmap];0.95[JPT][hapmap]
rs6499563	0.80[EUR][1000 genomes]
rs6680	0.81[JPT][hapmap]
rs7184169	0.81[JPT][hapmap]
rs7185840	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7186155	0.81[EUR][1000 genomes]
rs7188962	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7189115	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7189591	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7190994	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7190995	0.81[JPT][hapmap]
rs7191127	0.81[JPT][hapmap]
rs7192848	0.85[JPT][hapmap]
rs7194397	0.82[ASN][1000 genomes]
rs7194668	0.80[ASN][1000 genomes]
rs7197020	0.80[EUR][1000 genomes]
rs7199261	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7201225	0.85[JPT][hapmap]
rs7201643	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7201866	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7202268	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7203426	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7203821	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7350838	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7940	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8044555	0.81[JPT][hapmap]
rs8044868	0.95[JPT][hapmap]
rs8050238	0.81[JPT][hapmap];0.88[YRI][hapmap]
rs8051882	0.81[JPT][hapmap]
rs8052338	0.90[JPT][hapmap]
rs8052408	0.81[GIH][hapmap];0.95[JPT][hapmap]
rs8053907	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8059437	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8060770	0.84[EUR][1000 genomes]
rs8062895	0.81[CHD][hapmap]
rs8182213	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9924964	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9926156	0.81[JPT][hapmap]
rs9926927	0.86[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs9927526	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs9928157	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9930890	0.86[ASN][1000 genomes]
rs9932951	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9936642	0.85[JPT][hapmap]
rs9938382	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9941087	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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
9	nsv906895	chr16:72083318-72106756	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
10	nsv906896	chr16:72083318-72114002	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7200854	FAM65A	cis	cerebellum	SCAN
rs7200854	DHODH	cis	cerebellum	SCAN
rs7200854	HPR	cis	parietal	SCAN
rs7200854	OR4D11	trans	cerebellum	SCAN
rs7200854	DHX38	cis	lymphoblastoid	seeQTL
rs7200854	HP	cis	cerebellum	SCAN
rs7200854	NRN1L	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72059600-72084600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr16:72060200-72095600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr16:72060200-72110600	Weak transcription	Esophagus	oesophagus
4	chr16:72076200-72098200	Weak transcription	Fetal Heart	heart
5	chr16:72076600-72084600	Weak transcription	Lung	lung
6	chr16:72076600-72092400	Weak transcription	Left Ventricle	heart
7	chr16:72077000-72107400	Weak transcription	Right Ventricle	heart
8	chr16:72077400-72084000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr16:72077400-72102400	Weak transcription	Brain Substantia Nigra	brain
10	chr16:72077400-72107400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr16:72077600-72084400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr16:72077600-72107400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr16:72078000-72083600	Weak transcription	Primary B cells from cord blood	blood
14	chr16:72078000-72084400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr16:72078000-72090000	Weak transcription	Gastric	stomach
16	chr16:72078000-72100800	Weak transcription	Brain Hippocampus Middle	brain
17	chr16:72078000-72103200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr16:72078200-72095600	Weak transcription	Brain Anterior Caudate	brain
19	chr16:72078200-72105200	Weak transcription	Brain Angular Gyrus	brain
20	chr16:72078400-72084600	Weak transcription	Adipose Nuclei	Adipose
21	chr16:72078400-72098400	Weak transcription	Primary T cells from cord blood	blood
22	chr16:72078400-72105400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr16:72078400-72108000	Weak transcription	Aorta	Aorta
24	chr16:72079600-72084000	Weak transcription	HepG2	liver
25	chr16:72082800-72084200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
26	chr16:72082800-72087800	Enhancers	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links