Variant report

Variant	rs3768372
Chromosome Location	chr1:226835632-226835633
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226834406..226836488-chr1:227013877..227016506,3	K562	blood:
2	chr1:226834406..226836185-chr1:227013877..227015402,2	K562	blood:
3	chr1:226834023..226836698-chr1:226841817..226845290,3	MCF-7	breast:
4	chr1:226834690..226837543-chr1:226839422..226842104,4	K562	blood:
5	chr1:226833813..226836204-chr1:226860352..226862883,2	K562	blood:

Variant related genes	Relation type
ENSG00000228382	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12077348	0.93[ASW][hapmap];0.85[CEU][hapmap];0.91[GIH][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs12405164	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12568026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2236604	0.97[CHD][hapmap];0.86[GIH][hapmap];0.90[LWK][hapmap];0.85[MEX][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs35483910	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738723	0.97[CHD][hapmap]
rs3754380	1.00[GIH][hapmap]
rs3754387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768371	0.81[ASW][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3768373	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820636	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][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	nsv873234	chr1:226779449-226859676	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv522446	chr1:226785530-226923938	Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv873235	chr1:226819073-226851963	Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3437235	chr1:226835029-226839227	ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3768372	CABC1	cis	parietal	SCAN
rs3768372	MOSC2	cis	cerebellum	SCAN
rs3768372	TLR5	cis	parietal	SCAN
rs3768372	PARP1	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226814200-226837600	Weak transcription	HUVEC	blood vessel
2	chr1:226814800-226840600	Weak transcription	Small Intestine	intestine
3	chr1:226816800-226837000	Weak transcription	Fetal Brain Male	brain
4	chr1:226817000-226837000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:226820400-226840800	Genic enhancers	Primary T cells fromperipheralblood	blood
6	chr1:226823200-226841400	Weak transcription	NHDF-Ad	bronchial
7	chr1:226823800-226837400	Strong transcription	Dnd41	blood
8	chr1:226824800-226836800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:226828000-226837200	Genic enhancers	Brain Hippocampus Middle	brain
10	chr1:226829400-226843800	Weak transcription	Brain Germinal Matrix	brain
11	chr1:226830400-226840400	Genic enhancers	Primary T cells from cord blood	blood
12	chr1:226830400-226840400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
13	chr1:226830600-226835800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:226830600-226838000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:226831200-226837400	Genic enhancers	Brain Substantia Nigra	brain
16	chr1:226831400-226841600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:226831800-226837000	Strong transcription	Fetal Intestine Small	intestine
18	chr1:226832000-226836000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:226832000-226838400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr1:226832000-226843800	Weak transcription	HMEC	breast
21	chr1:226832200-226836000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:226832200-226837200	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:226832200-226837400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:226832400-226836000	Strong transcription	Pancreas	Pancrea
25	chr1:226832400-226836200	Strong transcription	Fetal Lung	lung
26	chr1:226832400-226836600	Strong transcription	Fetal Intestine Large	intestine
27	chr1:226832400-226837400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
28	chr1:226832400-226843600	Weak transcription	Stomach Mucosa	stomach
29	chr1:226832800-226837400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:226832800-226837400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr1:226833000-226837000	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr1:226833000-226837200	Strong transcription	Duodenum Mucosa	Duodenum
33	chr1:226833000-226838800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
34	chr1:226833400-226837000	Strong transcription	Gastric	stomach
35	chr1:226833400-226837200	Strong transcription	GM12878-XiMat	blood
36	chr1:226833400-226837400	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr1:226833400-226837400	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr1:226833600-226835800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr1:226833600-226836600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:226833600-226844000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:226833800-226836200	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:226833800-226837400	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr1:226833800-226838200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:226833800-226841600	Weak transcription	Fetal Heart	heart
45	chr1:226834000-226835800	Strong transcription	Colonic Mucosa	Colon
46	chr1:226834000-226836600	Strong transcription	Brain Anterior Caudate	brain
47	chr1:226834000-226836800	Strong transcription	Adipose Nuclei	Adipose
48	chr1:226834000-226837000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:226834000-226837400	Weak transcription	Right Atrium	heart
50	chr1:226834200-226836600	Strong transcription	Liver	Liver

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