Variant report

Variant	rs2236914
Chromosome Location	chr1:227078721-227078722
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227076139..227079788-chr1:227081535..227086284,4	K562	blood:
2	chr1:227068805..227071011-chr1:227076122..227078773,2	K562	blood:

Variant related genes	Relation type
ENSG00000163050	Chromatin interaction
ENSG00000143801	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1046240	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1150897	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1150900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11802358	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs12086302	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12758915	0.87[EUR][1000 genomes]
rs1289395	0.82[EUR][1000 genomes]
rs1289396	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1295638	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][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]
rs1295640	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]
rs1295641	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1295643	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1295647	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1296171	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1794038	0.93[EUR][1000 genomes]
rs1800674	0.87[EUR][1000 genomes]
rs2073489	0.90[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2236915	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];0.97[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]
rs2246221	0.85[CEU][hapmap];0.81[GIH][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs2793461	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2802268	0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2855559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2855560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2855562	0.87[EUR][1000 genomes]
rs2855564	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653470	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6426547	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6426548	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6674701	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6688068	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6692729	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6697001	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6697431	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6759	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];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7514364	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7518926	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7530245	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7530370	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7547071	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8383	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2236914	PSEN2	Cis_1M	lymphoblastoid	RTeQTL
rs2236914	PSEN2	cis	lymphoblastoid	seeQTL
rs2236914	ARF1	cis	cerebellum	SCAN
rs2236914	ZNF74	trans	parietal	SCAN
rs2236914	PSEN2	cis	parietal	SCAN
rs2236914	PSEN2	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227059800-227095000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:227063000-227081400	Weak transcription	Psoas Muscle	Psoas
3	chr1:227067000-227081400	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:227069400-227085000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:227069400-227087800	Weak transcription	HMEC	breast
6	chr1:227069400-227102800	Weak transcription	K562	blood
7	chr1:227070000-227079800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:227070400-227079000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:227070800-227088200	Weak transcription	Fetal Brain Male	brain
10	chr1:227071000-227089000	Strong transcription	Stomach Smooth Muscle	stomach
11	chr1:227071200-227086800	Weak transcription	NHDF-Ad	bronchial
12	chr1:227071200-227088400	Weak transcription	Hela-S3	cervix
13	chr1:227071200-227091400	Weak transcription	Osteobl	bone
14	chr1:227071400-227079000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:227071400-227079600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:227071400-227080000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr1:227071400-227084400	Strong transcription	Fetal Intestine Small	intestine
18	chr1:227071600-227087000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:227071800-227102400	Weak transcription	Small Intestine	intestine
20	chr1:227072200-227087000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:227072200-227091800	Weak transcription	Fetal Kidney	kidney
22	chr1:227072200-227100400	Weak transcription	Stomach Mucosa	stomach
23	chr1:227072800-227083600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:227073000-227078800	Strong transcription	HSMMtube	muscle
25	chr1:227073000-227080400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:227073000-227085200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:227073200-227079600	Weak transcription	Thymus	Thymus
28	chr1:227073400-227084400	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:227073400-227084600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:227073400-227088600	Strong transcription	Fetal Stomach	stomach
31	chr1:227073400-227092200	Strong transcription	Pancreas	Pancrea
32	chr1:227073800-227100600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr1:227074200-227080400	Strong transcription	Brain Anterior Caudate	brain
34	chr1:227074200-227081800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:227074200-227083000	Strong transcription	Colon Smooth Muscle	Colon
36	chr1:227074200-227091800	Weak transcription	Fetal Heart	heart
37	chr1:227074600-227079600	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr1:227074600-227079800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr1:227074800-227090000	Weak transcription	Primary B cells from peripheral blood	blood
40	chr1:227074800-227090200	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:227075000-227079200	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:227075000-227084200	Strong transcription	Gastric	stomach
43	chr1:227075000-227085400	Strong transcription	Ovary	ovary
44	chr1:227075000-227087400	Weak transcription	Primary B cells from cord blood	blood
45	chr1:227075000-227088800	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:227075200-227079600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr1:227075200-227079600	Strong transcription	Left Ventricle	heart
48	chr1:227075200-227079800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr1:227075200-227081200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:227075200-227083200	Strong transcription	H9 Cell Line	embryonic stem cell

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