Variant report

Variant	rs2572344
Chromosome Location	chr4:48988705-48988706
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10024211	0.82[CEU][hapmap]
rs10027569	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs10222924	0.85[ASW][hapmap];0.83[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap]
rs1051447	0.85[ASW][hapmap];0.83[CEU][hapmap];0.89[GIH][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap]
rs11410065	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11730515	0.89[GIH][hapmap]
rs12499992	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12502614	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12505576	0.89[GIH][hapmap]
rs13124375	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13135263	0.96[GIH][hapmap];0.88[TSI][hapmap]
rs13141488	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1350122	0.83[CEU][hapmap];0.99[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1350123	0.96[GIH][hapmap];0.88[TSI][hapmap]
rs1455937	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861606	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17611143	0.85[ASW][hapmap];0.83[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap]
rs1840628	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1993383	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2572343	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2572357	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2572358	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2572359	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2572361	0.85[AMR][1000 genomes]
rs2572362	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2572363	0.85[AMR][1000 genomes]
rs2605233	0.85[ASW][hapmap];0.83[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.96[MKK][hapmap];0.83[TSI][hapmap]
rs2605236	0.89[GIH][hapmap]
rs2605238	0.89[GIH][hapmap]
rs2605239	0.89[GIH][hapmap]
rs2605243	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2605244	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2605273	0.85[AMR][1000 genomes]
rs2605274	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2605275	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2768957	0.85[ASW][hapmap];0.83[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.96[MKK][hapmap];0.83[TSI][hapmap]
rs2768958	0.89[GIH][hapmap]
rs2768965	0.85[ASW][hapmap];0.83[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.96[MKK][hapmap];0.83[TSI][hapmap]
rs2768966	0.83[CEU][hapmap]
rs2768968	0.89[GIH][hapmap]
rs2768969	0.89[GIH][hapmap]
rs2768971	0.89[GIH][hapmap]
rs2768973	0.85[ASW][hapmap];0.83[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.96[MKK][hapmap]
rs28590759	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761728	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4552435	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695414	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4695415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695416	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4695417	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4695418	0.82[CEU][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes]
rs4695419	0.91[GIH][hapmap]
rs6822902	0.89[GIH][hapmap]
rs6824559	0.92[AMR][1000 genomes]
rs6850199	1.00[ASW][hapmap];0.83[CEU][hapmap];0.96[GIH][hapmap];0.93[LWK][hapmap];0.80[MEX][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7655341	0.89[GIH][hapmap]
rs7674928	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs936134	0.83[CEU][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs936135	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[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]
rs9683541	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9683610	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1003718	chr4:48771947-49083089	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv916809	chr4:48784318-49083302	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1011910	chr4:48784332-49154757	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv879010	chr4:48794403-49061141	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv427680	chr4:48829607-49660117	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
13	nsv1004364	chr4:48961611-49083089	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
14	esv1798238	chr4:48979634-48993377	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	esv1819278	chr4:48979634-48993377	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	esv1839152	chr4:48979634-48993377	Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv441875	chr4:48979634-48993377	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2572344	SLAIN2	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48987600-48988800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr4:48987600-48988800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr4:48987600-48988800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr4:48987600-48988800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr4:48987600-48988800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
6	chr4:48987600-48988800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr4:48987600-48989200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:48987600-48989200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:48987800-48988800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:48987800-48988800	Enhancers	Pancreas	Pancrea
11	chr4:48987800-48989000	Bivalent Enhancer	Fetal Brain Male	brain
12	chr4:48987800-48989800	Active TSS	Rectal Smooth Muscle	rectum
13	chr4:48988000-48988800	Bivalent/Poised TSS	Stomach Mucosa	stomach
14	chr4:48988000-48989200	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr4:48988200-48989200	Bivalent/Poised TSS	NHEK	skin
16	chr4:48988200-48990000	Active TSS	Colonic Mucosa	Colon
17	chr4:48988600-48988800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
18	chr4:48988600-48988800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:48988600-48988800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr4:48988600-48988800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
21	chr4:48988600-48988800	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr4:48988600-48988800	Enhancers	Liver	Liver
23	chr4:48988600-48988800	Bivalent Enhancer	Brain Hippocampus Middle	brain
24	chr4:48988600-48988800	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
25	chr4:48988600-48988800	Bivalent/Poised TSS	HMEC	breast
26	chr4:48988600-48989000	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr4:48988600-48989000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
28	chr4:48988600-48989000	Active TSS	Esophagus	oesophagus
29	chr4:48988600-48989000	Active TSS	Rectal Mucosa Donor 31	rectum
30	chr4:48988600-49000400	Weak transcription	Gastric	stomach

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