Variant report

Variant	rs1220405
Chromosome Location	chr1:9922245-9922246
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:9882600..9885826-chr1:9921034..9924372,4	MCF-7	breast:
2	chr1:9916480..9919428-chr1:9921291..9923091,2	K562	blood:
3	chr1:9921008..9924998-chr1:9925415..9929659,6	K562	blood:
4	chr1:9910251..9913174-chr1:9920173..9922421,2	K562	blood:
5	chr1:9881352..9884024-chr1:9922177..9924275,2	K562	blood:
6	chr1:9921625..9924250-chr1:9926048..9928989,2	K562	blood:
7	chr1:9907349..9914090-chr1:9919874..9926540,9	K562	blood:

Variant related genes	Relation type
ENSG00000223989	Chromatin interaction
ENSG00000171603	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1220381	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1220382	0.85[EUR][1000 genomes]
rs1220383	0.80[CEU][hapmap]
rs1220384	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1220392	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1220393	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1220394	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1220395	1.00[CEU][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs1220396	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1220404	0.88[TSI][hapmap]
rs1220406	0.94[EUR][1000 genomes]
rs1220411	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1220412	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.91[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1220413	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1220418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1372106	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1470160	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs15177	0.84[CHB][hapmap]
rs1660735	0.88[EUR][1000 genomes]
rs17034420	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs2083577	0.83[EUR][1000 genomes]
rs2278611	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs2379108	0.85[EUR][1000 genomes]
rs2486084	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2582980	0.85[EUR][1000 genomes]
rs2582981	0.84[EUR][1000 genomes]
rs3120822	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3860318	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs3888014	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs6695334	0.84[CHB][hapmap];0.81[CHD][hapmap]
rs7225	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs935073	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935074	0.90[EUR][1000 genomes]
rs935075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs946275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv871146	chr1:9897001-9951288	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv545380	chr1:9918183-9987007	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	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
rs1220405	NPPB	cis	parietal	SCAN
rs1220405	LOC440563	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9904000-9929800	Weak transcription	Aorta	Aorta
2	chr1:9904200-9927400	Weak transcription	Colonic Mucosa	Colon
3	chr1:9904200-9927800	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:9904400-9922600	Weak transcription	Pancreas	Pancrea
5	chr1:9904400-9923400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr1:9904400-9927800	Weak transcription	Stomach Mucosa	stomach
7	chr1:9904400-9930000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr1:9904600-9922600	Weak transcription	Ovary	ovary
9	chr1:9904600-9935000	Weak transcription	Osteobl	bone
10	chr1:9904800-9946000	Weak transcription	Fetal Kidney	kidney
11	chr1:9906600-9927400	Weak transcription	Liver	Liver
12	chr1:9907000-9930000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:9907400-9929800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:9910000-9935000	Weak transcription	NHLF	lung
15	chr1:9911000-9927400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr1:9911000-9930400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:9911200-9932400	Weak transcription	Fetal Heart	heart
18	chr1:9911400-9922600	Weak transcription	Right Ventricle	heart
19	chr1:9911400-9927200	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr1:9912200-9929600	Weak transcription	Primary B cells from cord blood	blood
21	chr1:9912200-9929600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:9912600-9927000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:9913000-9922600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:9913200-9923600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:9913400-9927400	Weak transcription	Fetal Brain Male	brain
26	chr1:9913600-9923600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:9913600-9927800	Weak transcription	Brain Angular Gyrus	brain
28	chr1:9914000-9927200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr1:9914000-9927400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:9914000-9927400	Weak transcription	Dnd41	blood
31	chr1:9914000-9927800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:9914000-9929600	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr1:9914000-9929800	Weak transcription	Primary T cells from cord blood	blood
34	chr1:9914200-9922600	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr1:9914200-9926800	Weak transcription	Fetal Lung	lung
36	chr1:9914400-9922400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:9915800-9928400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:9915800-9935200	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr1:9917800-9925200	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr1:9917800-9934400	Strong transcription	Fetal Intestine Small	intestine
41	chr1:9918000-9932800	Strong transcription	Fetal Brain Female	brain
42	chr1:9918200-9924400	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr1:9918200-9932800	Strong transcription	Lung	lung
44	chr1:9918400-9923600	Weak transcription	Psoas Muscle	Psoas
45	chr1:9918600-9923600	Strong transcription	Fetal Stomach	stomach
46	chr1:9918600-9943800	Weak transcription	Small Intestine	intestine
47	chr1:9918800-9925800	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr1:9919000-9923000	Weak transcription	Fetal Thymus	thymus
49	chr1:9919200-9922600	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr1:9919400-9926000	Weak transcription	Primary hematopoietic stem cells	blood

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