Variant report

Variant	rs10888435
Chromosome Location	chr1:151772475-151772476
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151771040..151773951-chr1:151782694..151784484,3	K562	blood:
2	chr1:151770881..151774367-chr1:151786518..151790478,5	MCF-7	breast:
3	chr1:151770963..151775334-chr1:151775936..151780512,5	MCF-7	breast:
4	chr1:151771155..151774343-chr1:151777363..151779853,3	MCF-7	breast:
5	chr1:151763150..151767122-chr1:151771180..151776437,5	K562	blood:
6	chr1:151771964..151773618-chr1:151776379..151779150,2	K562	blood:
7	chr1:151772358..151773986-chr1:151801710..151803954,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143365	Chromatin interaction
ENSG00000203288	Chromatin interaction
ENSG00000213171	Chromatin interaction
ENSG00000182134	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10494269	0.84[JPT][hapmap]
rs11204885	0.83[JPT][hapmap]
rs11204887	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11204888	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12066445	0.88[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs12073999	0.90[EUR][1000 genomes]
rs12409493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12567867	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1521177	0.89[JPT][hapmap]
rs1781419	0.83[CEU][hapmap];0.84[JPT][hapmap];0.93[EUR][1000 genomes]
rs2293088	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs33911740	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3748612	0.88[CEU][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap];0.92[EUR][1000 genomes]
rs3923394	0.83[CEU][hapmap];0.94[EUR][1000 genomes]
rs4845572	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6667279	0.92[EUR][1000 genomes]
rs6679233	0.88[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap]
rs7534811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs868868	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9017	0.96[CEU][hapmap];0.98[EUR][1000 genomes]
rs9826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010398	chr1:151761649-151790940	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10888435	TDRKH	Cis_1M	lymphoblastoid	RTeQTL
rs10888435	SNX27	cis	Esophagus Mucosa	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151764200-151772800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr1:151764200-151772800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:151764200-151772800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:151764200-151773000	Weak transcription	Thymus	Thymus
5	chr1:151764200-151778800	Weak transcription	Pancreas	Pancrea
6	chr1:151764200-151779600	Weak transcription	Gastric	stomach
7	chr1:151764200-151787000	Weak transcription	Right Ventricle	heart
8	chr1:151764200-151792800	Weak transcription	Lung	lung
9	chr1:151764400-151779200	Weak transcription	Liver	Liver
10	chr1:151764400-151779800	Weak transcription	Brain Angular Gyrus	brain
11	chr1:151764600-151779400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:151764600-151779400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:151764600-151782000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:151764600-151787600	Weak transcription	Primary T cells from cord blood	blood
15	chr1:151765000-151779400	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:151765400-151772800	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr1:151765400-151784200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:151766000-151772600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:151766000-151780200	Weak transcription	Dnd41	blood
20	chr1:151770400-151776200	Weak transcription	Spleen	Spleen
21	chr1:151770800-151787200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:151771400-151773400	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr1:151771400-151773600	Enhancers	Fetal Thymus	thymus
24	chr1:151771400-151778200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:151771600-151772600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
26	chr1:151771600-151772800	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr1:151771600-151773200	Enhancers	Placenta	Placenta
28	chr1:151771800-151772600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:151772000-151772600	Bivalent Enhancer	NHEK	skin
30	chr1:151772000-151774200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:151772200-151773600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
32	chr1:151772200-151777600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr1:151772400-151772800	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr1:151772400-151772800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:151772400-151773400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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