Variant report

Variant	rs1209264
Chromosome Location	chr1:154305010-154305011
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154154470..154156180-chr1:154303921..154306139,2	MCF-7	breast:
2	chr1:154304058..154305639-chr19:47729768..47731392,2	K562	blood:
3	chr1:154193867..154196410-chr1:154304631..154306238,2	K562	blood:
4	chr1:154297523..154301046-chr1:154302603..154305255,3	K562	blood:

Variant related genes	Relation type
ENSG00000143549	Chromatin interaction
ENSG00000143515	Chromatin interaction
ENSG00000265134	Chromatin interaction
ENSG00000105327	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11265608	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1194591	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs12024903	1.00[ASN][1000 genomes]
rs12026876	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12033701	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1205591	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1685633	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481065	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58548028	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72696301	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72698115	0.82[EUR][1000 genomes]
rs73026617	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9651036	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9651053	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9651055	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
8	nsv523934	chr1:154296076-154307630	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1209264	IL6R	Cis_1M	lymphoblastoid	RTeQTL
rs1209264	TARS2	cis	parietal	SCAN
rs1209264	C1orf85	cis	parietal	SCAN
rs1209264	S100A10	cis	cerebellum	SCAN
rs1209264	GATAD2B	cis	parietal	SCAN
rs1209264	C1orf230	cis	parietal	SCAN
rs1209264	C1orf43	cis	parietal	SCAN
rs1209264	BNIPL	cis	parietal	SCAN
rs1209264	SCARNA4	cis	cerebellum	SCAN
rs1209264	GOLPH3L	cis	cerebellum	SCAN
rs1209264	PIP5K1A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154301000-154308400	Weak transcription	Fetal Kidney	kidney
2	chr1:154301400-154318400	Weak transcription	Small Intestine	intestine
3	chr1:154301800-154306800	Weak transcription	Right Atrium	heart
4	chr1:154301800-154307400	Weak transcription	Pancreas	Pancrea
5	chr1:154302000-154306800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:154302200-154312200	Weak transcription	Gastric	stomach
7	chr1:154302200-154312600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:154302200-154322400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:154302400-154305400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:154302400-154305400	Strong transcription	Colon Smooth Muscle	Colon
11	chr1:154302400-154305600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:154302400-154306000	Strong transcription	NHLF	lung
13	chr1:154302400-154306400	Weak transcription	Liver	Liver
14	chr1:154302400-154306400	Strong transcription	NHDF-Ad	bronchial
15	chr1:154302400-154322400	Strong transcription	Dnd41	blood
16	chr1:154302400-154323200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:154302600-154306200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:154302600-154306200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:154302600-154306400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:154302600-154306400	Strong transcription	Stomach Smooth Muscle	stomach
21	chr1:154302600-154306600	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:154302600-154307000	Strong transcription	Fetal Stomach	stomach
23	chr1:154302600-154309800	Weak transcription	Fetal Brain Male	brain
24	chr1:154302600-154314400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:154302600-154318200	Weak transcription	Fetal Heart	heart
26	chr1:154302600-154320800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:154302600-154322600	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:154302600-154323000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:154302800-154305400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:154302800-154305800	Strong transcription	Placenta	Placenta
31	chr1:154302800-154306600	Strong transcription	Osteobl	bone
32	chr1:154302800-154307600	Strong transcription	Aorta	Aorta
33	chr1:154302800-154307800	Strong transcription	Brain Germinal Matrix	brain
34	chr1:154302800-154323000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:154303000-154305400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:154303000-154305400	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr1:154303000-154305400	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr1:154303000-154305400	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:154303000-154305400	Strong transcription	GM12878-XiMat	blood
40	chr1:154303000-154305400	Strong transcription	HUVEC	blood vessel
41	chr1:154303000-154305600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:154303000-154306400	Strong transcription	Brain Substantia Nigra	brain
43	chr1:154303000-154306600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:154303000-154306800	Strong transcription	Brain Anterior Caudate	brain
45	chr1:154303000-154306800	Strong transcription	Brain Hippocampus Middle	brain
46	chr1:154303000-154313000	Weak transcription	Colonic Mucosa	Colon
47	chr1:154303000-154322200	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr1:154303000-154322600	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr1:154303200-154305200	Strong transcription	NH-A	brain
50	chr1:154303200-154305600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood

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