Variant report

Variant	rs9473901
Chromosome Location	chr6:13289322-13289323
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13287477..13291631-chr6:13573758..13576939,3	K562	blood:
2	chr6:13272685..13275870-chr6:13286064..13289898,4	K562	blood:
3	chr6:13287888..13289538-chr6:13307383..13309880,2	K562	blood:

Variant related genes	Relation type
ENSG00000124523	Chromatin interaction
ENSG00000112137	Chromatin interaction
ENSG00000215022	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12203576	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202020	0.89[ASN][1000 genomes]
rs2439546	0.86[ASN][1000 genomes]
rs2496143	0.84[ASN][1000 genomes]
rs364884	0.89[ASN][1000 genomes]
rs381134	0.89[ASN][1000 genomes]
rs3846903	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs384730	0.86[ASN][1000 genomes]
rs408639	0.89[ASN][1000 genomes]
rs408923	0.89[ASN][1000 genomes]
rs412787	0.86[ASN][1000 genomes]
rs417048	0.86[ASN][1000 genomes]
rs421057	0.86[ASN][1000 genomes]
rs442614	0.86[ASN][1000 genomes]
rs446843	0.89[ASN][1000 genomes]
rs4605869	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs543645	0.87[EUR][1000 genomes]
rs546520	0.89[ASN][1000 genomes]
rs561549	0.85[EUR][1000 genomes]
rs570338	0.89[ASN][1000 genomes]
rs617580	0.81[AFR][1000 genomes]
rs629262	0.89[ASN][1000 genomes]
rs629728	0.88[ASN][1000 genomes]
rs641293	0.89[ASN][1000 genomes]
rs641688	0.89[ASN][1000 genomes]
rs6910418	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7774863	0.89[ASN][1000 genomes]
rs878698	0.89[ASN][1000 genomes]
rs9381915	0.87[ASN][1000 genomes]
rs9473896	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9473901	RP1-257A7.5	cis	Thyroid	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13270200-13291600	Weak transcription	HSMM	muscle
2	chr6:13273800-13291400	Weak transcription	Psoas Muscle	Psoas
3	chr6:13274600-13302000	Weak transcription	Small Intestine	intestine
4	chr6:13274800-13292800	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:13275600-13291600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:13280000-13292600	Weak transcription	NHLF	lung
7	chr6:13280200-13292400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:13282800-13289400	Strong transcription	Right Ventricle	heart
9	chr6:13282800-13291600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:13283600-13289600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:13284000-13293000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr6:13284000-13294200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:13285000-13289600	ZNF genes & repeats	Fetal Intestine Small	intestine
14	chr6:13285400-13302400	Weak transcription	HUVEC	blood vessel
15	chr6:13285800-13289800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:13285800-13293000	Weak transcription	Brain Angular Gyrus	brain
17	chr6:13285800-13293000	Weak transcription	Brain Substantia Nigra	brain
18	chr6:13286600-13291600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:13286600-13292800	Weak transcription	Colonic Mucosa	Colon
20	chr6:13286800-13289400	ZNF genes & repeats	Fetal Intestine Large	intestine
21	chr6:13287000-13289600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
22	chr6:13287000-13289800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:13287000-13289800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
24	chr6:13287000-13289800	Strong transcription	Gastric	stomach
25	chr6:13287000-13289800	ZNF genes & repeats	Thymus	Thymus
26	chr6:13287000-13303600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:13287200-13290000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:13287200-13292000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr6:13287200-13292800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr6:13287400-13294400	Weak transcription	Fetal Kidney	kidney
31	chr6:13287800-13291800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:13287800-13294200	Weak transcription	A549	lung
33	chr6:13287800-13295200	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr6:13287800-13298200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr6:13288000-13289400	Weak transcription	NHDF-Ad	bronchial
36	chr6:13288000-13289600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr6:13288000-13290600	Strong transcription	Left Ventricle	heart
38	chr6:13288000-13292200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr6:13288000-13294600	Weak transcription	Fetal Brain Male	brain
40	chr6:13288000-13296200	Strong transcription	Primary B cells from peripheral blood	blood
41	chr6:13288200-13289600	Strong transcription	Spleen	Spleen
42	chr6:13288200-13290000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:13288200-13290400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr6:13288200-13291600	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr6:13288200-13291600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:13288200-13291600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:13288200-13291600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:13288200-13291600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr6:13288200-13291600	Weak transcription	Brain Germinal Matrix	brain
50	chr6:13288200-13291600	Weak transcription	Brain Hippocampus Middle	brain

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