Variant report

Variant	rs7242978
Chromosome Location	chr18:44633424-44633425
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:44631824..44634440-chr18:44636514..44640477,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KATNAL2-5	chr18:44632317-44634433	ENSG00000267724.1

Variant related genes	Relation type
ENSG00000167220	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11663321	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12960378	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12960444	0.89[AFR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12963648	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12964465	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13381713	0.81[GIH][hapmap]
rs16954921	0.83[GIH][hapmap]
rs16954999	0.83[GIH][hapmap]
rs17785419	0.81[CEU][hapmap]
rs2251948	0.96[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2277717	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2461247	0.92[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2571001	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2571009	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576031	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2576053	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2576056	0.96[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2576060	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2635040	1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2635041	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2635042	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2635043	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2635045	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2635046	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs2635047	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2635049	0.96[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2635050	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2668761	0.83[GIH][hapmap]
rs2668779	0.84[EUR][1000 genomes]
rs2684818	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2684820	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2684822	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2684825	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2684826	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2684837	0.83[CEU][hapmap]
rs28693565	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28702976	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2932126	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3816125	1.00[CEU][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs4986203	0.82[TSI][hapmap]
rs7504798	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9304341	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9960264	1.00[CEU][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs9962602	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9629	chr18:44264693-44757511	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv833640	chr18:44552276-44714872	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv909612	chr18:44560875-44681485	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv576819	chr18:44602249-44677627	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7242978	KATNAL2	cis	parietal	SCAN
rs7242978	PIAS2	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44607600-44637600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr18:44609200-44638400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr18:44611600-44635600	Weak transcription	Psoas Muscle	Psoas
4	chr18:44613800-44638200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr18:44617200-44635400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr18:44620600-44635000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr18:44620800-44675400	Weak transcription	A549	lung
8	chr18:44621200-44634800	Weak transcription	Pancreas	Pancrea
9	chr18:44621400-44638600	Weak transcription	Colonic Mucosa	Colon
10	chr18:44621600-44674400	Weak transcription	Small Intestine	intestine
11	chr18:44623000-44637400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr18:44623200-44635200	Weak transcription	HepG2	liver
13	chr18:44623800-44635000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr18:44624200-44634800	Weak transcription	Gastric	stomach
15	chr18:44624200-44654200	Weak transcription	Fetal Heart	heart
16	chr18:44624400-44637400	Weak transcription	HMEC	breast
17	chr18:44624400-44640600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr18:44624600-44635000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr18:44626600-44664800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr18:44626800-44634600	Weak transcription	NHEK	skin
21	chr18:44626800-44637400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr18:44627000-44633600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr18:44627000-44635000	Weak transcription	Brain Germinal Matrix	brain
24	chr18:44627000-44636600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr18:44627200-44635200	Weak transcription	Fetal Intestine Small	intestine
26	chr18:44627200-44638000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr18:44627600-44633600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr18:44628200-44640200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr18:44628400-44637800	Weak transcription	GM12878-XiMat	blood
30	chr18:44628600-44635200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr18:44628600-44640000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr18:44628600-44640600	Weak transcription	Esophagus	oesophagus
33	chr18:44628600-44641400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr18:44629000-44637600	Weak transcription	NHDF-Ad	bronchial
35	chr18:44629200-44637800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr18:44629200-44675800	Weak transcription	HUVEC	blood vessel
37	chr18:44629400-44634800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr18:44629400-44635200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr18:44629400-44642200	Strong transcription	Liver	Liver
40	chr18:44629400-44642400	Strong transcription	Primary T cells from cord blood	blood
41	chr18:44629600-44635000	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr18:44629600-44640400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr18:44629800-44636600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr18:44629800-44642400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr18:44630000-44633600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr18:44630000-44633800	Strong transcription	Fetal Muscle Leg	muscle
47	chr18:44630000-44635000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr18:44630000-44641600	Strong transcription	Fetal Lung	lung
49	chr18:44630000-44641800	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr18:44630000-44641800	Strong transcription	Dnd41	blood

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