Variant report

Variant	rs3750359
Chromosome Location	chr9:96425363-96425364
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:19527393..19530181-chr9:96424975..96426814,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10117225	0.91[MEX][hapmap]
rs10122270	1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs10123378	0.90[MEX][hapmap]
rs10761240	0.91[MEX][hapmap]
rs10761249	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs10761250	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821168	0.86[MEX][hapmap]
rs10821185	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10821186	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10821187	0.92[EUR][1000 genomes]
rs10821188	0.92[EUR][1000 genomes]
rs10821189	0.92[EUR][1000 genomes]
rs10821190	0.96[EUR][1000 genomes]
rs10821191	0.96[CEU][hapmap];0.94[GIH][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs10821192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821193	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821194	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821195	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821202	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10821203	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10992797	0.91[MEX][hapmap]
rs10992812	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10992813	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10992815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10992819	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10992829	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992831	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992839	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992840	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992842	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992860	0.90[ASW][hapmap];0.92[CEU][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1132004	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1140722	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11534279	0.89[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs12238738	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1412048	0.81[MEX][hapmap]
rs1806524	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs2001315	0.91[EUR][1000 genomes]
rs2001589	0.96[CEU][hapmap];0.94[GIH][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs2001610	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2398848	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2398856	0.96[CEU][hapmap];0.94[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs34031628	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34103739	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35171420	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36013568	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3750354	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs3750357	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3829758	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036592	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7040340	0.96[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs7044244	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7851178	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7851271	0.92[EUR][1000 genomes]
rs7864397	0.96[CEU][hapmap];0.94[GIH][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs7865712	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs7868191	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs7871695	0.81[EUR][1000 genomes]

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	nsv893586	chr9:96363859-96493773	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv1036609	chr9:96375217-96477641	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv893587	chr9:96383605-96451784	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv972421	chr9:96413056-96428661	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv3341449	chr9:96421831-96426729	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3750359	HIATL1	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96400400-96430600	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr9:96401000-96430000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:96401000-96438600	Weak transcription	Psoas Muscle	Psoas
4	chr9:96402600-96430200	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr9:96402600-96433600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr9:96403400-96430800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr9:96403400-96430800	Strong transcription	Liver	Liver
8	chr9:96405200-96429200	Strong transcription	Duodenum Mucosa	Duodenum
9	chr9:96405200-96431400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr9:96405400-96430000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr9:96405400-96430600	Strong transcription	Primary T cells from cord blood	blood
12	chr9:96405400-96431400	Strong transcription	Fetal Brain Female	brain
13	chr9:96405400-96433200	Strong transcription	Fetal Intestine Small	intestine
14	chr9:96405600-96429800	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr9:96405600-96430000	Strong transcription	Brain Germinal Matrix	brain
16	chr9:96405600-96430400	Strong transcription	Stomach Smooth Muscle	stomach
17	chr9:96406200-96438600	Weak transcription	Small Intestine	intestine
18	chr9:96406800-96430600	Strong transcription	Brain Hippocampus Middle	brain
19	chr9:96407200-96430400	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr9:96410000-96430200	Strong transcription	Fetal Muscle Trunk	muscle
21	chr9:96410200-96428600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr9:96410400-96432600	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr9:96410400-96433200	Strong transcription	Gastric	stomach
24	chr9:96411800-96428600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr9:96412400-96430000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr9:96412600-96427600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr9:96412600-96430000	Weak transcription	K562	blood
28	chr9:96412600-96439400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr9:96412600-96442800	Weak transcription	NHDF-Ad	bronchial
30	chr9:96412600-96445000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr9:96412800-96425400	Weak transcription	Fetal Kidney	kidney
32	chr9:96412800-96425600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr9:96412800-96425800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr9:96412800-96427600	Weak transcription	Fetal Brain Male	brain
35	chr9:96412800-96430600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:96412800-96442800	Weak transcription	HMEC	breast
37	chr9:96412800-96443600	Weak transcription	Stomach Mucosa	stomach
38	chr9:96413000-96426000	Strong transcription	Esophagus	oesophagus
39	chr9:96413000-96432000	Strong transcription	Placenta	Placenta
40	chr9:96413000-96442000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr9:96413000-96444800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr9:96413200-96430800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr9:96413200-96440800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr9:96413400-96441600	Weak transcription	GM12878-XiMat	blood
45	chr9:96414200-96434800	Weak transcription	Right Atrium	heart
46	chr9:96414400-96435800	Weak transcription	HSMM	muscle
47	chr9:96415600-96426400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr9:96416400-96443400	Weak transcription	HepG2	liver
49	chr9:96416800-96426200	Strong transcription	Fetal Lung	lung
50	chr9:96417200-96425400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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