Variant report

Variant	rs12737638
Chromosome Location	chr1:214494006-214494007
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:214451643..214456693-chr1:214488650..214497237,17	MCF-7	breast:
2	chr1:214488324..214490814-chr1:214493702..214496792,3	MCF-7	breast:
3	chr1:214491130..214494829-chr1:214496540..214499830,3	K562	blood:
4	chr1:214474368..214476686-chr1:214492540..214494376,2	K562	blood:
5	chr1:214491270..214493161-chr1:214493280..214496080,3	K562	blood:

Variant related genes	Relation type
ENSG00000143499	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10864093	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10864094	0.87[ASN][1000 genomes]
rs11120289	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12081918	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12081925	0.94[ASN][1000 genomes]
rs12095774	0.92[ASN][1000 genomes]
rs12725392	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1874804	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2088512	0.94[ASN][1000 genomes]
rs34932055	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3754136	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3767843	0.86[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6676709	0.87[ASW][hapmap];0.98[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs6704032	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs870117	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12737638	KCTD3	cis	parietal	SCAN
rs12737638	SMYD2	Cis_1M	lymphoblastoid	RTeQTL
rs12737638	GALC	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:214471000-214517400	Weak transcription	Fetal Kidney	kidney
2	chr1:214477400-214506400	Weak transcription	Colon Smooth Muscle	Colon
3	chr1:214477400-214506400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr1:214477400-214511000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:214479000-214503000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:214482200-214510600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:214483600-214501600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:214484400-214499800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:214484400-214510800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:214484800-214501800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr1:214484800-214507800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:214484800-214522000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr1:214485000-214506400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:214485000-214513200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:214485600-214499600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:214485800-214499600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:214486200-214526000	Weak transcription	Psoas Muscle	Psoas
18	chr1:214487400-214502600	Weak transcription	Colonic Mucosa	Colon
19	chr1:214487400-214509400	Strong transcription	Primary T cells from cord blood	blood
20	chr1:214487600-214497400	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr1:214487600-214506200	Weak transcription	Small Intestine	intestine
22	chr1:214487800-214510600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:214488000-214496400	Strong transcription	Dnd41	blood
24	chr1:214488000-214497800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:214488200-214499000	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr1:214488200-214500400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:214488200-214517600	Weak transcription	Brain Germinal Matrix	brain
28	chr1:214488200-214520800	Weak transcription	Hela-S3	cervix
29	chr1:214488800-214497800	Strong transcription	Fetal Stomach	stomach
30	chr1:214488800-214510600	Weak transcription	Fetal Brain Male	brain
31	chr1:214489400-214506200	Weak transcription	A549	lung
32	chr1:214489400-214506600	Weak transcription	Ovary	ovary
33	chr1:214490200-214501800	Weak transcription	NHLF	lung
34	chr1:214490200-214502400	Weak transcription	Placenta	Placenta
35	chr1:214490400-214502400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:214490600-214496400	Strong transcription	Primary B cells from cord blood	blood
37	chr1:214490800-214518200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr1:214491000-214503400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr1:214491200-214495800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr1:214491200-214497000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:214491600-214506000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr1:214491800-214495400	Strong transcription	NHEK	skin
43	chr1:214491800-214500400	Weak transcription	HUVEC	blood vessel
44	chr1:214492000-214494400	Strong transcription	Primary B cells from peripheral blood	blood
45	chr1:214492000-214494800	Weak transcription	GM12878-XiMat	blood
46	chr1:214492200-214495400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:214492200-214496200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:214492400-214494400	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr1:214492400-214495000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr1:214492400-214495800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links