Variant report

Variant	rs2108971
Chromosome Location	chr17:19565945-19565946
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:19564551..19566163-chr17:19566583..19568566,2	MCF-7	breast:
2	chr17:19558329..19562006-chr17:19563141..19565959,3	MCF-7	breast:
3	chr17:19552711..19555521-chr17:19564350..19566731,2	MCF-7	breast:
4	chr17:19565101..19568606-chr17:19573068..19575796,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264932	Chromatin interaction
ENSG00000072210	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11204408	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11656199	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11656773	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11871420	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12150145	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12941194	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17684040	0.91[EUR][1000 genomes]
rs1812051	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2120274	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2165895	0.90[EUR][1000 genomes]
rs2245639	0.91[EUR][1000 genomes]
rs2386141	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386142	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386143	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386145	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];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2440162	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2453586	0.91[EUR][1000 genomes]
rs2453600	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2453601	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2453604	0.91[EUR][1000 genomes]
rs2453608	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28495827	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28537694	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3760489	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4273101	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4925036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56109259	0.90[EUR][1000 genomes]
rs62065943	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62065946	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6587200	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6587201	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7210433	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7215	0.85[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7405861	0.86[EUR][1000 genomes]
rs7405862	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7502992	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8069478	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8069576	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[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8074500	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8074784	0.84[EUR][1000 genomes]
rs8079648	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8081130	1.00[JPT][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.80[YRI][hapmap]
rs962800	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9889632	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9903027	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428337	chr17:19340045-19585774	Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482827	chr17:19456848-19645771	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1061408	chr17:19458185-19613357	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1055361	chr17:19515267-19582503	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	nsv1062485	chr17:19558644-19608008	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv907865	chr17:19558722-19575721	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1063892	chr17:19564634-19808485	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2108971	ALDH3A2	cis	multi-tissue	Pritchard
rs2108971	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL
rs2108971	MAP2K3	cis	cerebellum	SCAN
rs2108971	PIGL	cis	parietal	SCAN
rs2108971	ALDH3A2	cis	parietal	SCAN
rs2108971	ALDH3A2	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19553200-19566800	Weak transcription	Primary B cells from cord blood	blood
2	chr17:19553200-19577400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr17:19553200-19580000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr17:19553400-19566400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr17:19554800-19574400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr17:19555000-19568800	Weak transcription	NH-A	brain
7	chr17:19555000-19581800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr17:19555000-19582800	Weak transcription	HUVEC	blood vessel
9	chr17:19555200-19566400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr17:19555200-19566600	Weak transcription	NHDF-Ad	bronchial
11	chr17:19555200-19569800	Strong transcription	Fetal Muscle Trunk	muscle
12	chr17:19555200-19576400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr17:19555400-19570000	Strong transcription	Fetal Muscle Leg	muscle
14	chr17:19555600-19567200	Weak transcription	Right Atrium	heart
15	chr17:19555600-19569800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr17:19555600-19578600	Weak transcription	Small Intestine	intestine
17	chr17:19556200-19569800	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr17:19556600-19569800	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr17:19557200-19569800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr17:19558200-19568200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr17:19558200-19569400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr17:19558200-19569600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr17:19558200-19569800	Strong transcription	Fetal Intestine Large	intestine
24	chr17:19558400-19566600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr17:19558400-19566800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr17:19558400-19567200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr17:19558400-19571800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr17:19558400-19579200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr17:19558600-19569800	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr17:19558800-19566800	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr17:19559200-19571800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr17:19559200-19574200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr17:19559400-19566800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr17:19559400-19575000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr17:19559400-19575400	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr17:19559600-19570800	Strong transcription	Brain Anterior Caudate	brain
37	chr17:19559600-19578600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr17:19559800-19577200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr17:19560200-19566600	Weak transcription	Fetal Brain Male	brain
40	chr17:19560200-19566800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr17:19560200-19566800	Weak transcription	Right Ventricle	heart
42	chr17:19560400-19566600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr17:19560600-19566400	Weak transcription	Fetal Heart	heart
44	chr17:19560800-19566400	Weak transcription	Brain Substantia Nigra	brain
45	chr17:19560800-19566600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr17:19560800-19566600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr17:19560800-19567000	Weak transcription	Psoas Muscle	Psoas
48	chr17:19560800-19567400	Weak transcription	Placenta	Placenta
49	chr17:19561200-19567000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr17:19561200-19570600	Strong transcription	Monocytes-CD14+_RO01746	blood

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