Variant report

Variant	rs10761374
Chromosome Location	chr9:97834573-97834574
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97488120..97490104-chr9:97832042..97834756,2	MCF-7	breast:
2	chr9:97834530..97836565-chr9:97839818..97842096,2	MCF-7	breast:
3	chr9:97769187..97771943-chr9:97834202..97836015,2	MCF-7	breast:
4	chr9:97821556..97825075-chr9:97832512..97834984,3	MCF-7	breast:
5	chr9:97829667..97831442-chr9:97833759..97836647,2	MCF-7	breast:
6	chr9:97825460..97828452-chr9:97831131..97835733,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1011784	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10739992	0.86[JPT][hapmap];0.84[LWK][hapmap]
rs10821447	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10821455	0.86[JPT][hapmap]
rs1979022	0.86[JPT][hapmap]
rs2166402	0.86[JPT][hapmap];0.84[LWK][hapmap]
rs2297596	0.86[JPT][hapmap]
rs2297597	0.86[JPT][hapmap]
rs3277	0.86[JPT][hapmap]
rs3737142	0.86[JPT][hapmap]
rs3780564	0.86[JPT][hapmap]
rs3780568	0.86[JPT][hapmap];0.82[LWK][hapmap]
rs3844341	0.86[JPT][hapmap]
rs3852402	0.86[JPT][hapmap]
rs4647459	0.86[JPT][hapmap]
rs4647462	0.86[JPT][hapmap]
rs4647475	0.86[JPT][hapmap]
rs4647528	0.86[JPT][hapmap];0.82[LWK][hapmap]
rs4647554	0.86[JPT][hapmap];0.89[LWK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs4647558	0.86[JPT][hapmap]
rs4657	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4743988	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744442	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744446	0.86[JPT][hapmap]
rs6479598	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7034538	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs7042293	0.88[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7042320	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7046682	0.94[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7850958	0.86[JPT][hapmap]
rs7854570	0.86[JPT][hapmap]
rs7874388	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs963774	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
2	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
5	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10761374	AUH	cis	cerebellum	SCAN
rs10761374	NINJ1	cis	cerebellum	SCAN
rs10761374	TDRD7	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97813000-97873000	Weak transcription	K562	blood
2	chr9:97820000-97854200	Weak transcription	Fetal Brain Male	brain
3	chr9:97820400-97840800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr9:97820400-97843000	Weak transcription	Primary T cells from cord blood	blood
5	chr9:97820600-97875000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr9:97821000-97838400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr9:97821200-97839000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr9:97821200-97839600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:97821400-97843200	Weak transcription	Fetal Brain Female	brain
10	chr9:97821800-97835600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:97822000-97834600	Strong transcription	Hela-S3	cervix
12	chr9:97822800-97845400	Weak transcription	Primary B cells from cord blood	blood
13	chr9:97823600-97834600	Strong transcription	NH-A	brain
14	chr9:97823600-97845000	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr9:97824800-97844600	Weak transcription	Fetal Thymus	thymus
16	chr9:97825200-97841000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:97825400-97854400	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr9:97825800-97839200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:97825800-97843400	Weak transcription	Thymus	Thymus
20	chr9:97825800-97852600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr9:97826000-97842800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr9:97826200-97843200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr9:97826200-97847400	Weak transcription	HUVEC	blood vessel
24	chr9:97826400-97842800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr9:97826400-97844200	Weak transcription	GM12878-XiMat	blood
26	chr9:97826600-97835200	Weak transcription	Spleen	Spleen
27	chr9:97827000-97839600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:97827600-97835600	Enhancers	Right Atrium	heart
29	chr9:97827800-97841400	Genic enhancers	Liver	Liver
30	chr9:97828200-97838800	Strong transcription	Fetal Intestine Large	intestine
31	chr9:97829200-97838400	Genic enhancers	Brain Hippocampus Middle	brain
32	chr9:97829800-97835600	Enhancers	Rectal Smooth Muscle	rectum
33	chr9:97829800-97838000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr9:97830600-97835200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr9:97830600-97835200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr9:97830600-97843200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr9:97830600-97844800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr9:97830800-97837200	Genic enhancers	Ovary	ovary
39	chr9:97830800-97838600	Strong transcription	Osteobl	bone
40	chr9:97830800-97840800	Strong transcription	NHEK	skin
41	chr9:97831000-97836000	Enhancers	Psoas Muscle	Psoas
42	chr9:97831000-97839000	Genic enhancers	Left Ventricle	heart
43	chr9:97831200-97836400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr9:97831200-97841200	Genic enhancers	Pancreas	Pancrea
45	chr9:97832000-97836200	Enhancers	Brain Cingulate Gyrus	brain
46	chr9:97832000-97838000	Weak transcription	Stomach Mucosa	stomach
47	chr9:97832000-97838400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
48	chr9:97832200-97836200	Weak transcription	Fetal Lung	lung
49	chr9:97832200-97840800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr9:97832200-97841000	Enhancers	Fetal Heart	heart

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