Variant report

Variant	rs5997509
Chromosome Location	chr22:30128179-30128180
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30126165..30128637-chr22:30161660..30163491,2	MCF-7	breast:
2	chr22:30123279..30125899-chr22:30126231..30128918,2	K562	blood:
3	chr22:30127476..30130014-chr22:30183535..30186061,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100319	Chromatin interaction
ENSG00000184076	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1001318	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12159536	0.89[ASN][1000 genomes]
rs12163073	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs13057811	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2232903	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34347404	0.86[EUR][1000 genomes]
rs5997507	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5997508	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs5997515	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs5997518	0.89[ASN][1000 genomes]
rs6006229	0.88[EUR][1000 genomes]
rs6006238	0.89[ASN][1000 genomes]
rs6006239	0.89[ASN][1000 genomes]
rs6006241	0.89[ASN][1000 genomes]
rs71331211	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7290420	0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv914963	chr22:30075052-30133579	Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv914964	chr22:30081715-30150549	Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv515720	chr22:30081715-30163526	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv914966	chr22:30088442-30138548	Weak transcription Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1065072	chr22:30102176-30155245	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv471194	chr22:30103476-30128380	Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv471195	chr22:30103476-30128380	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv914967	chr22:30103476-30133579	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30117000-30137200	Weak transcription	HSMM	muscle
2	chr22:30117200-30133800	Weak transcription	Right Atrium	heart
3	chr22:30122400-30129400	Weak transcription	Colon Smooth Muscle	Colon
4	chr22:30123000-30129600	Weak transcription	Brain Angular Gyrus	brain
5	chr22:30123000-30135400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr22:30123200-30129200	Weak transcription	Fetal Brain Male	brain
7	chr22:30123200-30129600	Weak transcription	Colonic Mucosa	Colon
8	chr22:30123200-30130600	Weak transcription	NH-A	brain
9	chr22:30123200-30131800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr22:30123200-30135800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr22:30123200-30137600	Weak transcription	Osteobl	bone
12	chr22:30123200-30142800	Weak transcription	Brain Substantia Nigra	brain
13	chr22:30123400-30129400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr22:30123600-30130000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr22:30123600-30133400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr22:30123600-30134000	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr22:30123600-30135600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr22:30123600-30146800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr22:30123600-30147000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr22:30123800-30130600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr22:30123800-30136600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr22:30124000-30129600	Weak transcription	Psoas Muscle	Psoas
23	chr22:30124000-30129600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr22:30124200-30131000	Strong transcription	Brain Germinal Matrix	brain
25	chr22:30124400-30129200	Strong transcription	Fetal Stomach	stomach
26	chr22:30124600-30129000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr22:30124600-30130400	Weak transcription	Primary B cells from peripheral blood	blood
28	chr22:30124600-30133600	Weak transcription	Fetal Lung	lung
29	chr22:30124600-30136600	Weak transcription	Primary B cells from cord blood	blood
30	chr22:30124800-30129400	Weak transcription	NHEK	skin
31	chr22:30124800-30130400	Strong transcription	Spleen	Spleen
32	chr22:30124800-30135200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr22:30125000-30129000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr22:30125000-30129600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr22:30125000-30135600	Weak transcription	Dnd41	blood
36	chr22:30125200-30131600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr22:30125400-30129200	Strong transcription	Ovary	ovary
38	chr22:30125400-30130000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr22:30125400-30130600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr22:30125400-30146200	Weak transcription	NHLF	lung
41	chr22:30125600-30129000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr22:30125600-30132400	Strong transcription	Lung	lung
43	chr22:30125800-30128200	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr22:30125800-30132400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr22:30126000-30129800	Strong transcription	Brain Hippocampus Middle	brain
46	chr22:30126000-30144600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr22:30126200-30128200	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr22:30126200-30129600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr22:30126200-30132200	Strong transcription	Thymus	Thymus
50	chr22:30126400-30128600	Strong transcription	Stomach Smooth Muscle	stomach

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