Variant report

Variant	rs1331378
Chromosome Location	chr9:5935900-5935901
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10117416	0.94[EUR][1000 genomes]
rs10121480	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10733517	1.00[CEU][hapmap]
rs10733520	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10733522	0.94[EUR][1000 genomes]
rs10733523	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs10739079	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10739082	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10758731	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10758732	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs10758734	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10815330	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10815335	1.00[CEU][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes]
rs12335590	0.95[YRI][hapmap]
rs12338275	0.95[YRI][hapmap]
rs1331379	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[EUR][1000 genomes]
rs1418740	1.00[CEU][hapmap]
rs1478935	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1478936	0.94[EUR][1000 genomes]
rs1478937	0.86[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs1478938	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs16923578	1.00[CEU][hapmap]
rs16923633	0.85[YRI][hapmap]
rs186913	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[EUR][1000 genomes]
rs1888703	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs1888704	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2150703	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs2169906	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2244053	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs2244058	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs2291055	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap]
rs2381341	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2381360	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2890690	0.94[EUR][1000 genomes]
rs343469	1.00[CEU][hapmap]
rs343471	1.00[CEU][hapmap]
rs343480	1.00[CEU][hapmap]
rs343482	1.00[CEU][hapmap]
rs343500	1.00[CEU][hapmap];0.81[YRI][hapmap]
rs3739649	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[EUR][1000 genomes]
rs3933800	0.83[ASN][1000 genomes]
rs4075225	1.00[CEU][hapmap]
rs4265236	1.00[CEU][hapmap]
rs4389996	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs4395943	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs4740833	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4740834	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4742131	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4742142	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4742143	0.80[ASN][1000 genomes]
rs58909954	0.92[ASN][1000 genomes]
rs6477017	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs6477021	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6477022	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6477023	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6477024	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6477025	0.94[EUR][1000 genomes]
rs6477026	0.94[EUR][1000 genomes]
rs7019606	1.00[CEU][hapmap]
rs7021498	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7024130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7026453	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7026454	0.81[CHB][hapmap];0.80[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7029054	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7029833	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7030731	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7032130	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7034210	1.00[CEU][hapmap]
rs7042947	1.00[CEU][hapmap]
rs7044750	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7851749	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7856075	0.90[ASN][1000 genomes]
rs7866793	1.00[CEU][hapmap]
rs7868062	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7869571	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7875450	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017103	chr9:5509431-5987907	Weak transcription Strong transcription Flanking Active TSS Enhancers 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	31 gene(s)	inside rSNPs	diseases
2	nsv539965	chr9:5509431-5987907	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv892155	chr9:5825768-6044937	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv892156	chr9:5892375-6011757	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1015450	chr9:5915640-6114652	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
9	nsv613204	chr9:5931216-5971977	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:5898400-5947200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr9:5919000-5939800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:5920800-5938800	Weak transcription	Small Intestine	intestine
4	chr9:5921200-5939800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr9:5921200-5950400	Weak transcription	Psoas Muscle	Psoas
6	chr9:5922000-5941600	Weak transcription	HSMMtube	muscle
7	chr9:5922400-5939800	Weak transcription	Gastric	stomach
8	chr9:5922600-5947000	Weak transcription	Fetal Heart	heart
9	chr9:5923000-5936200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr9:5923000-5945200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr9:5923000-5969000	Weak transcription	Fetal Stomach	stomach
12	chr9:5923200-5938800	Weak transcription	Right Ventricle	heart
13	chr9:5923200-5939000	Weak transcription	Lung	lung
14	chr9:5923200-5939600	Weak transcription	Brain Angular Gyrus	brain
15	chr9:5923200-5943000	Weak transcription	Esophagus	oesophagus
16	chr9:5923200-5947600	Weak transcription	Fetal Kidney	kidney
17	chr9:5923200-5949200	Weak transcription	NHLF	lung
18	chr9:5923200-5968200	Weak transcription	Fetal Muscle Leg	muscle
19	chr9:5923200-5971800	Weak transcription	NHEK	skin
20	chr9:5923200-5972400	Weak transcription	Aorta	Aorta
21	chr9:5923400-5939400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr9:5923400-5939600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr9:5924600-5939600	Weak transcription	Brain Hippocampus Middle	brain
24	chr9:5924600-5942600	Weak transcription	Brain Germinal Matrix	brain
25	chr9:5924600-5945200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr9:5924600-5946800	Weak transcription	Brain Substantia Nigra	brain
27	chr9:5924600-5949200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr9:5924600-5967400	Weak transcription	Brain Anterior Caudate	brain
29	chr9:5924600-5968600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr9:5924600-5977000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr9:5924600-5977000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr9:5924800-5937800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr9:5924800-5942000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr9:5924800-5967600	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr9:5925000-5936000	Weak transcription	Primary B cells from peripheral blood	blood
36	chr9:5925200-5949200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr9:5925200-5968400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr9:5925400-5936200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr9:5926200-5952000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr9:5926800-5972600	Weak transcription	Fetal Intestine Small	intestine
41	chr9:5927400-5947800	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr9:5927600-5949000	Weak transcription	Primary T cells from cord blood	blood
43	chr9:5928000-5949200	Weak transcription	Ovary	ovary
44	chr9:5928400-5942400	Weak transcription	Fetal Brain Female	brain
45	chr9:5929000-5936200	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr9:5929000-5937400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr9:5929000-5944800	Weak transcription	GM12878-XiMat	blood
48	chr9:5929000-5948800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr9:5931400-5947800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr9:5931400-5950600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links