Variant report

Variant	rs10489332
Chromosome Location	chr1:174951068-174951069
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:174940091..174948288-chr1:174948961..174955449,13	K562	blood:
2	chr1:174950773..174953880-chr1:174954270..174959481,6	MCF-7	breast:
3	chr1:174948621..174950308-chr1:174951034..174953522,2	K562	blood:
4	chr1:174934157..174936495-chr1:174950544..174953349,2	K562	blood:

Variant related genes	Relation type
ENSG00000152061	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10489330	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11811190	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12140378	0.94[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs12737503	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs16847730	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2861102	0.85[ASN][1000 genomes]
rs2861106	0.88[CHB][hapmap]
rs3753562	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs41266060	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41266064	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41498747	0.88[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap]
rs4650666	1.00[YRI][hapmap]
rs58618779	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59436654	0.83[AFR][1000 genomes]
rs60893569	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6688577	0.85[YRI][hapmap]
rs6700434	0.88[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]

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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10489332	SLC9A11	cis	cerebellum	SCAN
rs10489332	SNORD78	cis	parietal	SCAN
rs10489332	RABGAP1L	Cis_1M	lymphoblastoid	RTeQTL
rs10489332	RABGAP1L	cis	normal skin	skin_eQTL
rs10489332	C1orf156	cis	parietal	SCAN
rs10489332	SELP	cis	cerebellum	SCAN

Chromatin state (count:114 , 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	chr1:174936000-174958600	Weak transcription	Brain Substantia Nigra	brain
13	chr1:174937000-174963600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:174937200-174955000	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:174937400-174963600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:174938000-174963600	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr1:174938600-174952000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:174938600-174959000	Weak transcription	Small Intestine	intestine
19	chr1:174938600-174959400	Weak transcription	Psoas Muscle	Psoas
20	chr1:174938600-174965200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:174938800-174951600	Weak transcription	Left Ventricle	heart
22	chr1:174938800-174959000	Weak transcription	Thymus	Thymus
23	chr1:174939400-174958800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:174940000-174967600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:174940600-174962000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:174940600-174963600	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:174941000-174951400	Weak transcription	Dnd41	blood
28	chr1:174941000-174968000	Weak transcription	Gastric	stomach
29	chr1:174941200-174951600	Weak transcription	Fetal Thymus	thymus
30	chr1:174941200-174952000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:174941200-174959600	Weak transcription	Colonic Mucosa	Colon
32	chr1:174941200-174959600	Weak transcription	Stomach Mucosa	stomach
33	chr1:174941400-174959400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr1:174941600-174951600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr1:174941800-174951800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr1:174941800-174952600	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr1:174942800-174957000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:174942800-174959000	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr1:174942800-174959600	Weak transcription	Right Ventricle	heart
40	chr1:174943400-174952000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr1:174943400-174952800	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr1:174943400-174954800	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr1:174943400-174955000	Strong transcription	Placenta	Placenta
44	chr1:174943800-174952400	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr1:174943800-174953600	Strong transcription	Duodenum Mucosa	Duodenum
46	chr1:174943800-174958600	Weak transcription	Colon Smooth Muscle	Colon
47	chr1:174944200-174959200	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr1:174944400-174959000	Weak transcription	Ovary	ovary
49	chr1:174944400-174967800	Weak transcription	Aorta	Aorta
50	chr1:174944800-174958800	Weak transcription	Rectal Smooth Muscle	rectum

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