Variant report

Variant	rs12729335
Chromosome Location	chr1:172510937-172510938
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:172509695..172512146-chr1:172529892..172531866,2	K562	blood:
2	chr1:172424143..172425875-chr1:172509096..172511619,2	K562	blood:
3	chr1:172510611..172514641-chr1:172517107..172521407,5	K562	blood:
4	chr1:172509473..172512440-chr1:172512519..172514495,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10489278	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10489279	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12724887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12727056	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12729948	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12730136	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12731039	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12731130	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12737154	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12739997	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12740436	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12743641	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12749864	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12750740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12752056	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12752646	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12753093	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12754650	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12756519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12758548	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12760161	0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17370159	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1984403	0.87[CEU][hapmap];0.92[JPT][hapmap]
rs2227189	0.92[ASN][1000 genomes]
rs2516064	0.88[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.93[ASN][1000 genomes]
rs3213552	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34134854	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35702642	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35780299	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3754424	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68164208	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs730278	0.85[ASN][1000 genomes]
rs7517917	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7549441	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs763109	0.85[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12729335	SNORD47	cis	cerebellum	SCAN
rs12729335	CD247	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172503400-172511200	Weak transcription	Spleen	Spleen
2	chr1:172503400-172511400	Weak transcription	Gastric	stomach
3	chr1:172503400-172528600	Weak transcription	Aorta	Aorta
4	chr1:172503400-172528600	Weak transcription	Lung	lung
5	chr1:172503600-172511400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:172503600-172511400	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr1:172503600-172513600	Weak transcription	Psoas Muscle	Psoas
8	chr1:172503600-172520200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:172503600-172531600	Weak transcription	Esophagus	oesophagus
10	chr1:172503800-172529000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:172503800-172534200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr1:172504000-172511600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:172504000-172524400	Weak transcription	HSMM	muscle
14	chr1:172504200-172515200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:172504200-172527000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr1:172504400-172519400	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr1:172504800-172511600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:172504800-172516200	Weak transcription	HUVEC	blood vessel
19	chr1:172505200-172518800	Weak transcription	Brain Angular Gyrus	brain
20	chr1:172505400-172511600	Weak transcription	Primary B cells from peripheral blood	blood
21	chr1:172505400-172511600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:172505800-172519600	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr1:172506000-172511600	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr1:172506000-172512000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:172506000-172519000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:172506000-172532600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:172506200-172511600	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr1:172506200-172511600	Weak transcription	Primary B cells from cord blood	blood
29	chr1:172506200-172525000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr1:172506200-172526200	Weak transcription	Fetal Intestine Large	intestine
31	chr1:172506200-172528400	Weak transcription	Fetal Stomach	stomach
32	chr1:172507000-172516000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:172507200-172516800	Weak transcription	Brain Germinal Matrix	brain
34	chr1:172507200-172518400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr1:172507400-172511600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:172507400-172513000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:172507400-172513400	Weak transcription	K562	blood
38	chr1:172507400-172513800	Weak transcription	Stomach Mucosa	stomach
39	chr1:172507400-172515000	Weak transcription	Right Atrium	heart
40	chr1:172507400-172516400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr1:172507400-172517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:172507400-172518400	Weak transcription	NHEK	skin
43	chr1:172507400-172523000	Weak transcription	NHDF-Ad	bronchial
44	chr1:172507400-172526400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr1:172507400-172528600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:172507600-172512000	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr1:172507600-172512000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:172507600-172512200	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr1:172508000-172517400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:172508200-172513000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links