Variant report

Variant	rs12761705
Chromosome Location	chr10:97920798-97920799
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:97914380..97917567-chr10:97919091..97921187,3	K562	blood:
2	chr10:97920196..97922493-chr10:97925714..97928075,3	K562	blood:
3	chr10:97848882..97852463-chr10:97918917..97921781,4	K562	blood:
4	chr10:97900100..97902878-chr10:97920561..97923291,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCNJ-1	chr10:97920102-97923508	ENSG00000177853

Variant related genes	Relation type
ENSG00000177853	Chromatin interaction
ENSG00000226688	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10491070	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];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10509695	1.00[JPT][hapmap]
rs10509700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10509701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10509703	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10882718	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs10882723	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882728	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11188575	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs11188596	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11188604	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs11188606	0.88[ASN][1000 genomes]
rs11188613	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs11188618	0.94[ASN][1000 genomes]
rs11188622	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188626	0.83[ASN][1000 genomes]
rs11188627	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11188631	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188632	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188635	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[ASN][1000 genomes]
rs11188656	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11591374	1.00[YRI][hapmap]
rs11591959	1.00[JPT][hapmap]
rs11593049	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11595809	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11596126	1.00[YRI][hapmap]
rs11597197	0.94[ASN][1000 genomes]
rs11598546	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11598837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11599170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11599662	1.00[YRI][hapmap]
rs12354644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12359842	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12411569	1.00[JPT][hapmap]
rs12768772	1.00[YRI][hapmap]
rs12771933	1.00[YRI][hapmap]
rs12778345	1.00[YRI][hapmap]
rs17382898	1.00[JPT][hapmap]
rs17383738	0.90[YRI][hapmap]
rs2039616	1.00[CHB][hapmap]
rs2125060	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3961944	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs4344425	1.00[JPT][hapmap]
rs60450792	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7081169	0.90[YRI][hapmap]
rs7096164	1.00[YRI][hapmap]
rs713070	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[ASN][1000 genomes]
rs7896077	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];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7916068	0.95[YRI][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12761705	GPR120	cis	cerebellum	SCAN
rs12761705	C10orf12	cis	cerebellum	SCAN
rs12761705	CRTAC1	cis	parietal	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97890800-97922400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:97891000-97927000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr10:97891800-97921400	Weak transcription	Stomach Mucosa	stomach
4	chr10:97892400-97924800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:97892800-97924200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr10:97903200-97923000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr10:97910800-97922200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr10:97911000-97921000	Strong transcription	Rectal Mucosa Donor 31	rectum
9	chr10:97911000-97921200	Strong transcription	Primary B cells from cord blood	blood
10	chr10:97911000-97921800	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr10:97911000-97921800	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr10:97911000-97921800	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr10:97911000-97922000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr10:97911000-97923000	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr10:97912400-97920800	Weak transcription	Right Ventricle	heart
16	chr10:97912400-97927800	Weak transcription	Fetal Brain Male	brain
17	chr10:97913000-97925400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr10:97914200-97924800	Weak transcription	Fetal Intestine Small	intestine
19	chr10:97914200-97925600	Weak transcription	Fetal Stomach	stomach
20	chr10:97914200-97925800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr10:97914200-97926200	Weak transcription	Pancreas	Pancrea
22	chr10:97914600-97921800	Weak transcription	Brain Germinal Matrix	brain
23	chr10:97915400-97923200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr10:97915400-97923400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr10:97916200-97921000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
26	chr10:97917200-97922200	Weak transcription	Colon Smooth Muscle	Colon
27	chr10:97917400-97921600	Weak transcription	Colonic Mucosa	Colon
28	chr10:97917400-97922800	Weak transcription	Fetal Heart	heart
29	chr10:97917400-97923000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr10:97917400-97928000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr10:97917600-97920800	Weak transcription	Brain Anterior Caudate	brain
32	chr10:97917600-97922600	Weak transcription	Ovary	ovary
33	chr10:97917600-97924800	Weak transcription	Small Intestine	intestine
34	chr10:97917600-97925200	Weak transcription	Fetal Brain Female	brain
35	chr10:97917600-97925800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr10:97917800-97920800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr10:97917800-97920800	Weak transcription	NHDF-Ad	bronchial
38	chr10:97917800-97921600	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr10:97918000-97923800	Weak transcription	HUVEC	blood vessel
40	chr10:97918000-97924200	Weak transcription	HSMM	muscle
41	chr10:97918000-97925400	Weak transcription	Brain Hippocampus Middle	brain
42	chr10:97918200-97924600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr10:97918200-97925400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr10:97918200-97925800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr10:97918200-97925800	Weak transcription	Osteobl	bone
46	chr10:97918200-97928000	Weak transcription	Thymus	Thymus
47	chr10:97918400-97921600	Weak transcription	Liver	Liver
48	chr10:97918400-97930000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr10:97918600-97921400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr10:97918600-97925400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links