Variant report

Variant	rs1295640
Chromosome Location	chr1:227070378-227070379
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1046240	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[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]
rs1150897	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1150900	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11802358	0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.88[ASN][1000 genomes]
rs12086302	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12758915	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1289395	0.83[EUR][1000 genomes]
rs1289396	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1295638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs1295641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1295643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1295647	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1296171	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1794038	0.93[EUR][1000 genomes]
rs1800674	0.87[EUR][1000 genomes]
rs2073489	0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.98[ASN][1000 genomes]
rs2236914	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2236915	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2246221	0.84[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs2793461	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802268	0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2855559	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2855560	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2855562	0.87[EUR][1000 genomes]
rs2855564	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4653470	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6426541	0.83[ASN][1000 genomes]
rs6426547	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6426548	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6674701	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6688068	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6692729	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6697001	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6697431	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6759	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]
rs7514364	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7518926	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7530245	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7530370	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7547071	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8383	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv4766	chr1:227025954-227070961	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1295640	ARF1	cis	cerebellum	SCAN
rs1295640	ZNF74	trans	parietal	SCAN
rs1295640	PSEN2	Cis_1M	lymphoblastoid	RTeQTL
rs1295640	PSEN2	cis	cerebellum	SCAN
rs1295640	PSEN2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227059800-227075600	Weak transcription	Brain Substantia Nigra	brain
2	chr1:227059800-227095000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:227060000-227070600	Weak transcription	Fetal Brain Male	brain
4	chr1:227060400-227073800	Weak transcription	HepG2	liver
5	chr1:227060400-227077600	Weak transcription	Brain Germinal Matrix	brain
6	chr1:227060600-227070400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr1:227060600-227070400	Weak transcription	HUVEC	blood vessel
8	chr1:227060600-227077400	Weak transcription	Fetal Brain Female	brain
9	chr1:227062200-227077400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:227062400-227073000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:227062400-227073000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:227063000-227081400	Weak transcription	Psoas Muscle	Psoas
13	chr1:227063800-227078000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:227064000-227070400	Weak transcription	NH-A	brain
15	chr1:227064000-227072600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr1:227064200-227070600	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:227064200-227070600	Weak transcription	Hela-S3	cervix
18	chr1:227064600-227073000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:227065400-227070800	Weak transcription	Brain Anterior Caudate	brain
20	chr1:227065800-227077400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:227066200-227072200	Strong transcription	H9 Cell Line	embryonic stem cell
22	chr1:227066800-227070800	Strong transcription	Aorta	Aorta
23	chr1:227066800-227071400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:227067000-227070800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:227067000-227071800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:227067000-227072000	Strong transcription	Brain Inferior Temporal Lobe	brain
27	chr1:227067000-227081400	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:227067200-227070400	Strong transcription	A549	lung
29	chr1:227067200-227072000	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr1:227067600-227071800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:227067800-227075400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:227068000-227070400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr1:227068200-227073400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:227068400-227070400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:227068400-227070400	Strong transcription	Pancreatic Islets	Pancreatic Islet
36	chr1:227068400-227071000	Strong transcription	Brain Cingulate Gyrus	brain
37	chr1:227068400-227071200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:227068600-227074200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:227068800-227072800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr1:227069000-227070400	Weak transcription	Ovary	ovary
41	chr1:227069000-227070400	Genic enhancers	NHLF	lung
42	chr1:227069000-227071200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:227069000-227071200	Weak transcription	Right Ventricle	heart
44	chr1:227069400-227070400	Enhancers	Esophagus	oesophagus
45	chr1:227069400-227070400	Genic enhancers	Pancreas	Pancrea
46	chr1:227069400-227074400	Enhancers	Fetal Thymus	thymus
47	chr1:227069400-227076000	Weak transcription	Brain Angular Gyrus	brain
48	chr1:227069400-227085000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:227069400-227087800	Weak transcription	HMEC	breast
50	chr1:227069400-227102800	Weak transcription	K562	blood

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