Variant report

Variant	rs10494951
Chromosome Location	chr1:212429259-212429260
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212427899..212432292-chr1:212432529..212438731,7	K562	blood:
2	chr1:212428875..212432292-chr1:212434801..212437724,6	K562	blood:
3	chr1:212422550..212424543-chr1:212427394..212429711,2	K562	blood:
4	chr1:212428170..212430153-chr1:212432529..212434264,2	K562	blood:
5	chr1:212409597..212412349-chr1:212428867..212431226,2	K562	blood:
6	chr1:212423429..212425837-chr1:212429181..212431560,2	K562	blood:

Variant related genes	Relation type
ENSG00000226251	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10863960	0.90[AFR][1000 genomes]
rs10863963	1.00[YRI][hapmap]
rs11119919	1.00[YRI][hapmap]
rs11119920	1.00[YRI][hapmap]
rs11119924	1.00[YRI][hapmap]
rs11576437	0.90[TSI][hapmap]
rs11580285	0.90[TSI][hapmap]
rs11587555	1.00[YRI][hapmap]
rs11588867	1.00[YRI][hapmap]
rs11589817	0.90[TSI][hapmap]
rs11590242	1.00[ASW][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs12726409	1.00[YRI][hapmap]
rs12727947	1.00[ASW][hapmap];0.85[LWK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs12728266	0.90[TSI][hapmap]
rs12730098	0.95[AFR][1000 genomes]
rs12743785	1.00[YRI][hapmap]
rs12745269	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs12746203	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12756678	1.00[YRI][hapmap]
rs17018997	0.81[TSI][hapmap]
rs17721302	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs2120770	0.84[TSI][hapmap]
rs2358448	1.00[YRI][hapmap]
rs34212128	1.00[AFR][1000 genomes]
rs34515259	0.84[AMR][1000 genomes]
rs34740542	0.90[AFR][1000 genomes]
rs35556190	0.84[AMR][1000 genomes]
rs6661987	1.00[YRI][hapmap]
rs6667199	1.00[YRI][hapmap]
rs6676208	0.90[TSI][hapmap]
rs6693849	1.00[YRI][hapmap]
rs6697910	0.81[TSI][hapmap]
rs71646153	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7518399	1.00[ASW][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs7533689	0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS 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	114 gene(s)	inside rSNPs	diseases
4	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS 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	45 gene(s)	inside rSNPs	diseases
5	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers 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	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10494951	CCL3L1	trans	brain	seeQTL
rs10494951	RP11-15I11.3	cis	lung	GTEx
rs10494951	IL8	trans	brain	seeQTL
rs10494951	RP11-15I11.3	cis	Adipose Subcutaneous	GTEx
rs10494951	RP11-15I11.3	cis	Thyroid	GTEx
rs10494951	KCNH1	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212416600-212430000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:212423600-212431200	Enhancers	Primary T cells fromperipheralblood	blood
3	chr1:212424400-212430800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr1:212424400-212431200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:212424600-212431000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:212426600-212430800	Enhancers	Fetal Thymus	thymus
7	chr1:212427400-212429600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:212427400-212429800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr1:212427400-212430400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:212427400-212430800	Enhancers	Primary B cells from peripheral blood	blood
11	chr1:212427600-212429600	Enhancers	Duodenum Mucosa	Duodenum
12	chr1:212427600-212430000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr1:212427600-212430200	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr1:212427600-212430400	Flanking Active TSS	Dnd41	blood
15	chr1:212427600-212430600	Enhancers	Thymus	Thymus
16	chr1:212428000-212431000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr1:212428200-212429400	Flanking Active TSS	Liver	Liver
18	chr1:212428200-212429400	Enhancers	Brain Angular Gyrus	brain
19	chr1:212428200-212429400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:212428200-212429400	Enhancers	Fetal Intestine Small	intestine
21	chr1:212428200-212429400	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr1:212428200-212429600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr1:212428200-212429600	Enhancers	Fetal Intestine Large	intestine
24	chr1:212428200-212429800	Enhancers	K562	blood
25	chr1:212428200-212430000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:212428200-212430000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:212428200-212430200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:212428200-212430200	Enhancers	Left Ventricle	heart
29	chr1:212428200-212430400	Enhancers	Brain Anterior Caudate	brain
30	chr1:212428200-212430400	Enhancers	GM12878-XiMat	blood
31	chr1:212428200-212430400	Flanking Active TSS	HepG2	liver
32	chr1:212428200-212430600	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr1:212428200-212430600	Enhancers	Lung	lung
34	chr1:212428200-212430800	Enhancers	Spleen	Spleen
35	chr1:212428200-212431000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr1:212428200-212431800	Enhancers	Pancreas	Pancrea
37	chr1:212428400-212429400	Weak transcription	Small Intestine	intestine
38	chr1:212428400-212430200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:212428400-212430200	Enhancers	Brain Substantia Nigra	brain
40	chr1:212428400-212430200	Enhancers	Colonic Mucosa	Colon
41	chr1:212428400-212430200	Enhancers	Placenta	Placenta
42	chr1:212428400-212430800	Enhancers	Right Ventricle	heart
43	chr1:212428600-212429400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:212428600-212429400	Enhancers	Brain Cingulate Gyrus	brain
45	chr1:212428600-212429400	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr1:212428600-212429800	Weak transcription	Right Atrium	heart
47	chr1:212428600-212430200	Enhancers	HSMM	muscle
48	chr1:212428600-212430400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr1:212428600-212434000	Weak transcription	Esophagus	oesophagus
50	chr1:212428800-212429600	Flanking Active TSS	Primary hematopoietic stem cells	blood

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