Variant report

Variant	rs10912862
Chromosome Location	chr1:174944764-174944765
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:174944582-174944872	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:174944704..174946274-chr1:174968716..174970697,2	MCF-7	breast:
2	chr1:174932689..174934966-chr1:174943606..174946963,3	K562	blood:
3	chr1:174927580..174945830-chr1:174955726..174971213,32	K562	blood:

Variant related genes	Relation type
RABGAP1L	TF binding region
ENSG00000252552	Chromatin interaction
ENSG00000152061	Chromatin interaction
ENSG00000116161	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10489331	0.83[ASW][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10489334	1.00[EUR][1000 genomes]
rs10912852	0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs10912866	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10912869	1.00[EUR][1000 genomes]
rs11806870	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs12061403	1.00[EUR][1000 genomes]
rs12062145	0.83[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12072529	1.00[ASW][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12075140	1.00[EUR][1000 genomes]
rs12089375	1.00[EUR][1000 genomes]
rs13376513	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847652	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16847670	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847689	1.00[EUR][1000 genomes]
rs16847701	0.88[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1894679	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4650677	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4651250	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs57512007	1.00[EUR][1000 genomes]
rs58503437	1.00[EUR][1000 genomes]
rs60411387	1.00[EUR][1000 genomes]
rs6425311	1.00[EUR][1000 genomes]
rs6689751	1.00[EUR][1000 genomes]
rs74128526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74128530	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1001000	chr1:174944208-174978853	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174910800-174957000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:174924200-174967800	Weak transcription	Brain Germinal Matrix	brain
3	chr1:174924400-174958200	Weak transcription	Fetal Brain Male	brain
4	chr1:174933000-174953600	Weak transcription	Fetal Heart	heart
5	chr1:174935000-174959000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr1:174935000-174964000	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:174935000-174967000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:174935200-174959000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr1:174935200-174959600	Weak transcription	Esophagus	oesophagus
10	chr1:174935400-174958400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr1:174935800-174959600	Weak transcription	Fetal Kidney	kidney
12	chr1:174936000-174945000	Weak transcription	NHEK	skin
13	chr1:174936000-174946200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:174936000-174950600	Weak transcription	Fetal Brain Female	brain
15	chr1:174936000-174958600	Weak transcription	Brain Substantia Nigra	brain
16	chr1:174936600-174945400	Weak transcription	Fetal Lung	lung
17	chr1:174937000-174963600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:174937200-174955000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:174937400-174963600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr1:174938000-174963600	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr1:174938400-174945600	Weak transcription	A549	lung
22	chr1:174938600-174945200	Weak transcription	Adipose Nuclei	Adipose
23	chr1:174938600-174952000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:174938600-174959000	Weak transcription	Small Intestine	intestine
25	chr1:174938600-174959400	Weak transcription	Psoas Muscle	Psoas
26	chr1:174938600-174965200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:174938800-174951600	Weak transcription	Left Ventricle	heart
28	chr1:174938800-174959000	Weak transcription	Thymus	Thymus
29	chr1:174939400-174958800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:174939600-174945600	Weak transcription	HSMM	muscle
31	chr1:174939600-174947800	Weak transcription	Liver	Liver
32	chr1:174940000-174967600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr1:174940600-174962000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:174940600-174963600	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:174941000-174944800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr1:174941000-174945200	Strong transcription	Fetal Intestine Small	intestine
37	chr1:174941000-174951400	Weak transcription	Dnd41	blood
38	chr1:174941000-174968000	Weak transcription	Gastric	stomach
39	chr1:174941200-174951600	Weak transcription	Fetal Thymus	thymus
40	chr1:174941200-174952000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:174941200-174959600	Weak transcription	Colonic Mucosa	Colon
42	chr1:174941200-174959600	Weak transcription	Stomach Mucosa	stomach
43	chr1:174941400-174945000	Weak transcription	Brain Anterior Caudate	brain
44	chr1:174941400-174959400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr1:174941600-174944800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:174941600-174945600	Weak transcription	HMEC	breast
47	chr1:174941600-174948200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:174941600-174948400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr1:174941600-174948400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:174941600-174948600	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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