Variant report

Variant	rs16890628
Chromosome Location	chr5:61612281-61612282
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:61611699..61613753-chr5:61626529..61628835,2	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1108158	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11740652	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11742167	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11747516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12655562	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13155253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13156073	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13156695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13161789	0.87[AMR][1000 genomes]
rs13162519	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13163533	0.86[EUR][1000 genomes]
rs13169321	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13170425	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13174779	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13176923	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13178729	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13181377	0.87[AMR][1000 genomes]
rs13189446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13190153	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs153860	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs153864	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.84[ASN][1000 genomes]
rs153866	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs153869	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap]
rs153873	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap]
rs16875037	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890613	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16890618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890651	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17382217	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs2059162	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2063255	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2272291	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2441115	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap]
rs246198	0.82[ASN][1000 genomes]
rs255391	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap]
rs26626	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs26627	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap]
rs27090	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.80[ASN][1000 genomes]
rs32047	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs34220654	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34596001	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35011	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs35012	1.00[CEU][hapmap];0.88[CHB][hapmap]
rs35058	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs35238667	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35311093	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35572300	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35672643	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35699711	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35744020	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35746052	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35794032	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35808056	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35815430	0.96[EUR][1000 genomes]
rs35842742	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36105063	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3776612	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3776614	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4289514	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6859822	0.86[AFR][1000 genomes]
rs71617425	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71617426	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71617427	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71617428	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71617429	0.88[EUR][1000 genomes]
rs7446543	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814169	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs971965	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]

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	nsv1024090	chr5:61258759-61921150	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2757996	chr5:61403138-61687817	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2759345	chr5:61403138-61748912	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv830318	chr5:61415713-61623320	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1020255	chr5:61451792-62031365	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1027539	chr5:61457762-62000008	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	esv2755585	chr5:61535831-61618595	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	nsv881726	chr5:61556730-61676911	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	nsv881727	chr5:61578041-61700970	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv1033578	chr5:61606610-61911153	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16890628	EGR4	trans	brain	seeQTL
rs16890628	ARC	trans	brain	seeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61603200-61629200	Weak transcription	Lung	lung
2	chr5:61603200-61629200	Weak transcription	Spleen	Spleen
3	chr5:61603400-61625200	Weak transcription	Stomach Mucosa	stomach
4	chr5:61603400-61658600	Weak transcription	Aorta	Aorta
5	chr5:61603600-61622200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:61603600-61622400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr5:61603600-61629200	Weak transcription	Psoas Muscle	Psoas
8	chr5:61603800-61629200	Weak transcription	Left Ventricle	heart
9	chr5:61604000-61617400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr5:61604000-61622200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr5:61604000-61622200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr5:61604000-61622200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr5:61604000-61629000	Weak transcription	Thymus	Thymus
14	chr5:61604200-61616800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr5:61604400-61616000	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr5:61604400-61617400	Weak transcription	Fetal Stomach	stomach
17	chr5:61604400-61617400	Weak transcription	HUVEC	blood vessel
18	chr5:61604400-61617600	Weak transcription	Placenta	Placenta
19	chr5:61604400-61627000	Weak transcription	Fetal Muscle Leg	muscle
20	chr5:61604400-61629200	Weak transcription	Esophagus	oesophagus
21	chr5:61604400-61629400	Weak transcription	Pancreas	Pancrea
22	chr5:61604400-61643800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr5:61604600-61612600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr5:61604600-61615400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr5:61604600-61615600	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr5:61604600-61616400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr5:61604600-61630000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr5:61604600-61658600	Weak transcription	Fetal Kidney	kidney
29	chr5:61604800-61614600	Weak transcription	Primary B cells from cord blood	blood
30	chr5:61604800-61615600	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr5:61605400-61617400	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr5:61605800-61617000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr5:61606000-61616400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr5:61606200-61614600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr5:61606400-61612600	Enhancers	Brain Cingulate Gyrus	brain
36	chr5:61606600-61612400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr5:61606600-61617600	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr5:61606600-61619600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr5:61606800-61629400	Weak transcription	Fetal Thymus	thymus
40	chr5:61607000-61617400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr5:61607200-61625000	Weak transcription	Fetal Brain Female	brain
42	chr5:61607200-61627200	Weak transcription	Fetal Lung	lung
43	chr5:61607200-61629200	Weak transcription	HSMMtube	muscle
44	chr5:61607800-61614400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr5:61607800-61614800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr5:61607800-61614800	Weak transcription	Small Intestine	intestine
47	chr5:61607800-61669400	Weak transcription	NHLF	lung
48	chr5:61608000-61623800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr5:61608800-61613400	Weak transcription	Fetal Heart	heart
50	chr5:61608800-61614600	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links