Variant report

Variant	rs3739748
Chromosome Location	chr9:97784009-97784010
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97765071..97767480-chr9:97781588..97784169,2	K562	blood:
2	chr9:97671639..97694679-chr9:97760418..97786060,142	MCF-7	breast:
3	chr9:97783764..97786051-chr9:97788470..97790440,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HIATL1-18	chr9:97783960-97784562	NONHSAT133342

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1020962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217441	1.00[CEU][hapmap]
rs1038092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10732407	1.00[CEU][hapmap]
rs10761362	1.00[CEU][hapmap]
rs10761371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993471	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12553869	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12555128	1.00[JPT][hapmap]
rs12555829	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1542108	1.00[CEU][hapmap]
rs1564235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571897	0.85[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16911834	1.00[JPT][hapmap]
rs16911856	1.00[JPT][hapmap]
rs1871220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888945	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888946	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061799	1.00[CEU][hapmap];0.86[MEX][hapmap];0.96[EUR][1000 genomes]
rs2061801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2104888	1.00[JPT][hapmap]
rs2306207	0.82[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs242448	1.00[JPT][hapmap]
rs356685	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs356686	1.00[JPT][hapmap]
rs3780560	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4332191	1.00[CEU][hapmap]
rs4743972	1.00[CEU][hapmap]
rs4743975	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[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743976	0.86[MEX][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4743977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743978	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743989	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4744421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744429	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4744437	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4744440	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs475413	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6479578	1.00[CEU][hapmap]
rs6479589	1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6479596	0.87[EUR][1000 genomes]
rs6479597	0.87[EUR][1000 genomes]
rs67134693	0.96[ASN][1000 genomes]
rs7019602	1.00[CEU][hapmap]
rs7022739	1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs7022963	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7023719	1.00[CEU][hapmap];0.86[MEX][hapmap]
rs7025100	1.00[CEU][hapmap]
rs7039768	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7046900	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs72750335	0.96[ASN][1000 genomes]
rs72750346	0.96[ASN][1000 genomes]
rs72750351	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72750359	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72750367	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72750373	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73540087	1.00[ASN][1000 genomes]
rs7867856	1.00[CEU][hapmap]
rs894426	1.00[CEU][hapmap]
rs9299427	0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97768000-97786200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr9:97768800-97785600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:97769000-97787600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:97769600-97784200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr9:97769600-97790200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr9:97770800-97810000	Weak transcription	Primary T cells from cord blood	blood
7	chr9:97773200-97793200	Weak transcription	Brain Germinal Matrix	brain
8	chr9:97776000-97784400	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr9:97776000-97784600	Strong transcription	Placenta	Placenta
10	chr9:97776400-97785400	Strong transcription	Fetal Intestine Large	intestine
11	chr9:97777400-97794200	Weak transcription	Thymus	Thymus
12	chr9:97778800-97786200	Genic enhancers	Osteobl	bone
13	chr9:97779400-97789200	Genic enhancers	Liver	Liver
14	chr9:97780200-97785200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr9:97780200-97788000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr9:97780200-97788200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr9:97780600-97786600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr9:97780600-97790800	Weak transcription	Fetal Brain Female	brain
19	chr9:97780800-97784400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr9:97780800-97786000	Genic enhancers	Left Ventricle	heart
21	chr9:97781000-97784200	Strong transcription	Hela-S3	cervix
22	chr9:97781000-97786400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr9:97781200-97785600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr9:97781200-97786400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr9:97781200-97787400	Genic enhancers	NHLF	lung
26	chr9:97781200-97793600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr9:97781400-97784600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:97781400-97785400	Genic enhancers	HSMM	muscle
29	chr9:97781400-97786200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr9:97781400-97793200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr9:97781400-97793600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:97781600-97784200	Genic enhancers	Ovary	ovary
33	chr9:97781600-97784200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
34	chr9:97781600-97784600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:97781600-97784600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr9:97781600-97784600	Strong transcription	Colonic Mucosa	Colon
37	chr9:97781600-97784800	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr9:97781600-97785000	Weak transcription	Small Intestine	intestine
39	chr9:97781600-97785400	Genic enhancers	Muscle Satellite Cultured Cells	--
40	chr9:97781600-97785400	Genic enhancers	NHDF-Ad	bronchial
41	chr9:97781600-97786200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr9:97781600-97787000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr9:97781600-97787200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr9:97781800-97784200	Genic enhancers	Brain Hippocampus Middle	brain
45	chr9:97781800-97784200	Enhancers	Right Atrium	heart
46	chr9:97781800-97784400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr9:97781800-97784400	Genic enhancers	HMEC	breast
48	chr9:97781800-97785000	Strong transcription	Fetal Stomach	stomach
49	chr9:97782000-97784200	Strong transcription	Fetal Muscle Trunk	muscle
50	chr9:97782000-97784400	Strong transcription	HUVEC	blood vessel

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