Variant report

Variant	rs41312176
Chromosome Location	chr9:71855270-71855271
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	chr9:71850777..71853807-chr9:71854436..71856252,3	K562	blood:
2	chr9:71854349..71857071-chr9:71859863..71862039,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-APBA1-6	chr9:71855143-71855736	NONHSAT131773

Variant related genes	Relation type
ENSG00000119139	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10867187	0.88[AMR][1000 genomes]
rs10867196	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12686420	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17062942	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2095876	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2282336	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2309421	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1035823	chr9:71465139-71901672	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv466396	chr9:71471912-71935577	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv614548	chr9:71471912-71935577	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats 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	25 gene(s)	inside rSNPs	diseases
7	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv893416	chr9:71597840-71888601	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
9	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv893427	chr9:71762766-71858517	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription 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	7 gene(s)	inside rSNPs	diseases
11	nsv1049943	chr9:71834295-71855369	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv831610	chr9:71846941-72016835	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71828000-71866000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr9:71828600-71856600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr9:71828600-71857600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr9:71828600-71865600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr9:71828800-71874200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr9:71831400-71868000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr9:71831400-71872800	Strong transcription	Liver	Liver
8	chr9:71831600-71863200	Weak transcription	Hela-S3	cervix
9	chr9:71834800-71856400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr9:71836400-71874000	Weak transcription	Fetal Brain Male	brain
11	chr9:71837400-71863000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr9:71838000-71861600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr9:71838600-71857600	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr9:71838600-71862200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:71839000-71857400	Strong transcription	HepG2	liver
16	chr9:71839000-71872600	Strong transcription	Fetal Intestine Large	intestine
17	chr9:71839600-71863400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr9:71839800-71856600	Strong transcription	HMEC	breast
19	chr9:71839800-71857600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:71839800-71857800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr9:71839800-71858000	Strong transcription	Adipose Nuclei	Adipose
22	chr9:71840000-71857400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr9:71840200-71855800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr9:71840200-71855800	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr9:71840200-71856000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:71840200-71856400	Strong transcription	HUVEC	blood vessel
27	chr9:71840200-71857400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr9:71840200-71858200	Strong transcription	Stomach Smooth Muscle	stomach
29	chr9:71840200-71858600	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr9:71840200-71870400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr9:71841000-71858000	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr9:71841400-71869800	Weak transcription	Colon Smooth Muscle	Colon
33	chr9:71841400-71869800	Weak transcription	K562	blood
34	chr9:71843000-71862400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:71843400-71855400	Weak transcription	Spleen	Spleen
36	chr9:71843400-71861600	Weak transcription	Primary B cells from cord blood	blood
37	chr9:71843400-71868000	Weak transcription	Dnd41	blood
38	chr9:71845200-71872000	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr9:71846600-71855800	Strong transcription	Fetal Lung	lung
40	chr9:71846800-71858200	Strong transcription	Duodenum Mucosa	Duodenum
41	chr9:71847000-71868800	Weak transcription	Small Intestine	intestine
42	chr9:71847200-71857800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr9:71847600-71855800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr9:71847600-71871200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr9:71847600-71879600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr9:71847800-71867800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr9:71848800-71856000	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr9:71848800-71857600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr9:71848800-71857800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr9:71849000-71855600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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