Variant report

Variant	rs1039916
Chromosome Location	chr8:8685854-8685855
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:8685713..8688062-chr8:8693014..8695350,2	K562	blood:
2	chr8:8680684..8683788-chr8:8684972..8687852,3	K562	blood:
3	chr8:8669602..8671376-chr8:8685847..8687587,2	K562	blood:

Extended variants
information (count: 75 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10046783	0.81[CHB][hapmap]
rs10046784	0.81[CHB][hapmap]
rs1039915	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1115138	0.81[CHB][hapmap]
rs11249891	0.84[EUR][1000 genomes]
rs11249893	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11775523	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11777085	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11783966	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs11784052	0.82[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12544992	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs12545499	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12547493	0.89[CEU][hapmap];0.83[CHB][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12677543	0.83[EUR][1000 genomes]
rs12677550	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs12682352	0.93[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs13254903	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs13259070	0.84[EUR][1000 genomes]
rs13259216	0.89[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13265731	0.83[CHB][hapmap]
rs1510934	0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs1533058	0.96[CEU][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1533059	0.96[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1567398	0.91[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1876836	0.80[CHB][hapmap]
rs2048419	0.86[EUR][1000 genomes]
rs2271342	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2409092	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2409096	0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs2428	0.81[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs332039	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs332040	0.89[CEU][hapmap];0.91[CHB][hapmap];0.80[CHD][hapmap];0.89[MEX][hapmap]
rs35039922	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35431455	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3789843	0.81[ASN][1000 genomes]
rs3789849	0.83[EUR][1000 genomes]
rs3827806	0.91[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs408459	0.91[CHB][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap]
rs435953	0.86[ASN][1000 genomes]
rs437895	0.91[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs4382480	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.81[ASN][1000 genomes]
rs440788	0.91[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs4481596	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4840362	0.82[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4841040	0.84[EUR][1000 genomes]
rs4841042	0.82[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs4841044	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs4841045	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4841051	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4841055	1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs57312668	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59046059	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60315134	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6601265	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6993494	0.83[CHB][hapmap];0.90[CHD][hapmap]
rs6994038	0.84[EUR][1000 genomes]
rs7006589	0.83[CHB][hapmap];0.90[CHD][hapmap]
rs7017599	0.81[ASN][1000 genomes]
rs7823757	0.80[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7832968	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs882462	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs907183	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers 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 miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1019606	chr8:8353661-8736992	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv539456	chr8:8353661-8736992	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv995047	chr8:8353662-8857913	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv1022511	chr8:8493992-8737132	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv539457	chr8:8493992-8737132	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	esv1824870	chr8:8583943-8699382	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	nsv831228	chr8:8608387-8790790	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv1018828	chr8:8609880-8790660	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv1022331	chr8:8610035-8787981	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers 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	4 gene(s)	inside rSNPs	diseases
11	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
12	nsv890338	chr8:8669622-8707970	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1015437	chr8:8681255-8723798	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1039916	TDH	cis	cerebellum	SCAN
rs1039916	MFHAS1	cis	cerebellum	SCAN
rs1039916	PRSS55	cis	cerebellum	SCAN
rs1039916	RP11-62H7.2	cis	Thyroid	GTEx
rs1039916	C8orf5	Cis_chr	lymphoblastoid	RTeQTL
rs1039916	FAM86B3P	cis	Esophagus Mucosa	GTEx
rs1039916	PPP1R3B	cis	cerebellum	SCAN
rs1039916	BLK	Cis_chr	lymphoblastoid	RTeQTL
rs1039916	FLJ10661	cis	cerebellum	SCAN
rs1039916	CTSB	cis	cerebellum	SCAN
rs1039916	SGK223	cis	Thyroid	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8658400-8687200	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr8:8663400-8691800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr8:8664200-8691400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr8:8664400-8691800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr8:8667200-8686200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr8:8667200-8699200	Weak transcription	Aorta	Aorta
7	chr8:8667200-8701600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr8:8667400-8686000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr8:8667400-8693400	Weak transcription	Small Intestine	intestine
10	chr8:8667600-8701000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr8:8670000-8701200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr8:8670200-8701200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr8:8670400-8705400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr8:8670800-8692400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr8:8671000-8692000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr8:8672000-8700200	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr8:8674800-8701800	Weak transcription	Primary T cells from cord blood	blood
18	chr8:8675200-8699000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr8:8675600-8686000	Weak transcription	Pancreas	Pancrea
20	chr8:8675800-8699800	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr8:8676200-8699400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr8:8676600-8691400	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr8:8677200-8686000	Weak transcription	Liver	Liver
24	chr8:8678000-8688000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr8:8678600-8694400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr8:8678800-8701600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr8:8679400-8686000	Weak transcription	Right Ventricle	heart
28	chr8:8679600-8701400	Weak transcription	A549	lung
29	chr8:8679600-8701600	Weak transcription	HepG2	liver
30	chr8:8680000-8686200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr8:8680400-8700200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr8:8680800-8687400	Weak transcription	Brain Angular Gyrus	brain
33	chr8:8681000-8686200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr8:8681800-8686200	Weak transcription	Brain Anterior Caudate	brain
35	chr8:8681800-8700000	Weak transcription	Fetal Thymus	thymus
36	chr8:8682200-8686200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr8:8683200-8691400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr8:8683200-8701400	Weak transcription	Fetal Intestine Small	intestine
39	chr8:8683800-8701000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr8:8684000-8686000	Weak transcription	K562	blood
41	chr8:8684000-8691800	Weak transcription	NHDF-Ad	bronchial
42	chr8:8684200-8700800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr8:8684600-8686200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr8:8684600-8691600	Weak transcription	HUVEC	blood vessel
45	chr8:8684600-8692000	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr8:8684600-8703800	Weak transcription	Dnd41	blood
47	chr8:8685400-8686400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr8:8685400-8686400	Enhancers	Rectal Smooth Muscle	rectum
49	chr8:8685400-8686600	Enhancers	Fetal Stomach	stomach
50	chr8:8685400-8686800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links