Variant report

Variant	rs11912198
Chromosome Location	chr22:29387370-29387371
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29379528..29381161-chr22:29385924..29388369,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs16986908	1.00[EUR][1000 genomes]
rs16986912	1.00[EUR][1000 genomes]
rs16986925	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs16986971	1.00[EUR][1000 genomes]
rs16986990	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4823000	0.89[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs5752840	1.00[JPT][hapmap]
rs5752848	0.96[ASN][1000 genomes]
rs5752850	1.00[ASW][hapmap];0.90[CHB][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5762883	0.91[JPT][hapmap]
rs5762922	0.88[ASN][1000 genomes]
rs5762923	0.80[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs5762925	0.80[LWK][hapmap]
rs5762926	0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5762928	0.80[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs5762929	0.90[CHB][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs5762930	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762931	0.90[CHB][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5762932	0.80[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs5762938	1.00[ASW][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5762944	0.96[ASN][1000 genomes]
rs7287755	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs8137391	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs8140640	0.89[ASW][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][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	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29365800-29394800	Weak transcription	Pancreas	Pancrea
2	chr22:29373400-29390800	Weak transcription	Hela-S3	cervix
3	chr22:29373600-29400200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr22:29374400-29395200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr22:29374600-29395600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr22:29374600-29400000	Weak transcription	Right Ventricle	heart
7	chr22:29374600-29401200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr22:29375600-29390800	Weak transcription	NHDF-Ad	bronchial
9	chr22:29375800-29395400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr22:29379600-29388400	Weak transcription	Psoas Muscle	Psoas
11	chr22:29379600-29400800	Weak transcription	Fetal Brain Female	brain
12	chr22:29380000-29388400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr22:29380800-29400800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr22:29381000-29388400	Weak transcription	Fetal Heart	heart
15	chr22:29381000-29393000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr22:29381000-29395600	Weak transcription	Esophagus	oesophagus
17	chr22:29381200-29400400	Weak transcription	Lung	lung
18	chr22:29381400-29389400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr22:29381600-29389000	Weak transcription	Dnd41	blood
20	chr22:29381600-29395400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr22:29381800-29388400	Weak transcription	Placenta	Placenta
22	chr22:29381800-29388400	Weak transcription	HSMMtube	muscle
23	chr22:29381800-29390600	Weak transcription	Colonic Mucosa	Colon
24	chr22:29382000-29387400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr22:29382000-29400200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr22:29382400-29393200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr22:29383000-29390000	Strong transcription	Fetal Intestine Small	intestine
28	chr22:29383200-29390000	Strong transcription	Fetal Stomach	stomach
29	chr22:29383400-29388400	Weak transcription	Gastric	stomach
30	chr22:29383400-29388600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr22:29383400-29400200	Weak transcription	Right Atrium	heart
32	chr22:29383600-29400400	Weak transcription	Aorta	Aorta
33	chr22:29383800-29388600	Weak transcription	Ovary	ovary
34	chr22:29383800-29395400	Weak transcription	NHEK	skin
35	chr22:29383800-29399800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr22:29383800-29400000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr22:29384600-29395600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr22:29384800-29388400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr22:29385000-29387800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr22:29385000-29395200	Weak transcription	Left Ventricle	heart
41	chr22:29385000-29395600	Weak transcription	A549	lung
42	chr22:29385200-29388600	Weak transcription	Brain Hippocampus Middle	brain
43	chr22:29385200-29388800	Weak transcription	Brain Angular Gyrus	brain
44	chr22:29385200-29388800	Strong transcription	HepG2	liver
45	chr22:29385600-29388400	Weak transcription	Brain Substantia Nigra	brain
46	chr22:29385600-29389800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr22:29385600-29394600	Weak transcription	Fetal Kidney	kidney
48	chr22:29385600-29395400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr22:29385600-29400800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr22:29385600-29401000	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links