Variant report

Variant	rs4788568
Chromosome Location	chr16:71913025-71913026
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:71912441..71914997-chr16:71916463..71919857,4	K562	blood:

Variant related genes	Relation type
ENSG00000182149	Chromatin interaction
ENSG00000102984	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10500567	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs10852505	1.00[CHB][hapmap]
rs11075910	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11639902	1.00[CHB][hapmap]
rs11642529	1.00[CHB][hapmap]
rs11644740	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs11648557	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs11865456	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12149307	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12149325	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12444594	0.94[EUR][1000 genomes]
rs12445564	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12445641	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12447045	0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs12448022	1.00[CHB][hapmap]
rs12708918	0.81[EUR][1000 genomes]
rs12708919	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs12934512	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs13332180	0.82[ASW][hapmap]
rs17286411	0.94[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs17357420	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs17358402	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs1834036	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2288030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs2878494	1.00[CHB][hapmap]
rs35619990	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3751820	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs4528577	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs4538017	0.82[ASW][hapmap]
rs4788450	0.88[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs4788561	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4788567	0.82[ASW][hapmap]
rs4788569	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788575	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4788579	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs7188591	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7195988	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7197486	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7198834	0.85[JPT][hapmap]
rs7202840	1.00[CHB][hapmap]
rs8044004	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8044335	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8049163	1.00[CHB][hapmap]
rs8050058	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs8051878	1.00[CHB][hapmap]
rs8052358	0.85[JPT][hapmap]
rs9932707	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9939911	0.85[JPT][hapmap]
rs9940234	1.00[CHB][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4788568	AARS	cis	parietal	SCAN
rs4788568	HPR	cis	cerebellum	SCAN
rs4788568	TMEM208	cis	parietal	SCAN
rs4788568	PDXDC2P	cis	cerebellum	SCAN
rs4788568	MARVELD3	cis	lymphoblastoid	seeQTL
rs4788568	PSMD7	cis	parietal	SCAN
rs4788568	MTSS1L	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71881200-71916600	Weak transcription	Small Intestine	intestine
2	chr16:71881800-71914400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr16:71881800-71914600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr16:71882000-71915600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr16:71882400-71914600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr16:71885600-71916600	Weak transcription	Stomach Mucosa	stomach
7	chr16:71888000-71914800	Weak transcription	HUVEC	blood vessel
8	chr16:71888000-71916400	Weak transcription	NHEK	skin
9	chr16:71891000-71914000	Strong transcription	Primary B cells from peripheral blood	blood
10	chr16:71894600-71916800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr16:71895800-71916400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr16:71896000-71913400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr16:71896000-71913800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr16:71896800-71916600	Weak transcription	NHLF	lung
15	chr16:71897800-71915600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr16:71898000-71916800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr16:71898200-71916600	Weak transcription	Psoas Muscle	Psoas
18	chr16:71898400-71916800	Weak transcription	Right Ventricle	heart
19	chr16:71898800-71914200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr16:71898800-71916400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr16:71898800-71916400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr16:71899000-71913200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr16:71899000-71913200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr16:71899000-71913400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr16:71899000-71913600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr16:71899000-71914200	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr16:71899000-71916600	Weak transcription	Esophagus	oesophagus
28	chr16:71899000-71917000	Weak transcription	Pancreas	Pancrea
29	chr16:71899200-71914200	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr16:71899400-71914400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr16:71899600-71914200	Weak transcription	Spleen	Spleen
32	chr16:71899600-71916600	Weak transcription	Colonic Mucosa	Colon
33	chr16:71899800-71916800	Weak transcription	Brain Substantia Nigra	brain
34	chr16:71900200-71917200	Weak transcription	Gastric	stomach
35	chr16:71901200-71914000	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr16:71902200-71913400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr16:71902200-71915200	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr16:71902200-71916800	Weak transcription	Aorta	Aorta
39	chr16:71902400-71913400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr16:71902600-71916600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr16:71904000-71916600	Weak transcription	Fetal Heart	heart
42	chr16:71904400-71914200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr16:71906000-71916000	Strong transcription	Fetal Stomach	stomach
44	chr16:71906400-71915400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr16:71907200-71914200	Strong transcription	Brain Germinal Matrix	brain
46	chr16:71907400-71913800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr16:71908000-71915800	Strong transcription	Fetal Muscle Trunk	muscle
48	chr16:71908200-71913600	Strong transcription	Fetal Brain Female	brain
49	chr16:71908200-71915000	Strong transcription	Brain Angular Gyrus	brain
50	chr16:71908400-71913200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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