Variant report

Variant	rs2041838
Chromosome Location	chr2:37468448-37468449
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr2:37468149-37468789	SK-N-SH	brain:	n/a	chr2:37468452-37468459
2	GATA3	chr2:37468134-37468800	SK-N-SH	brain:	n/a	chr2:37468452-37468459

No.	Distal block	Cell Line	Cell type
1	chr2:37458068..37462101-chr2:37468406..37471417,5	K562	blood:
2	chr2:37456368..37460350-chr2:37466636..37472512,8	MCF-7	breast:
3	chr2:37466438..37469109-chr2:37469695..37472739,3	K562	blood:
4	chr2:37466495..37468720-chr2:37469102..37471276,2	MCF-7	breast:

Variant related genes	Relation type
NDUFAF7	TF binding region
ENSG00000003509	Chromatin interaction
ENSG00000115816	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10201396	0.86[ASN][1000 genomes]
rs10204434	0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs10206380	0.81[JPT][hapmap]
rs10460527	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11124570	0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11124573	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1160516	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs11887618	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs12469082	0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs12471267	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12476195	0.98[ASN][1000 genomes]
rs13390055	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs13412560	0.95[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs13421912	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13429526	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17020344	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17020358	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2041839	0.99[ASN][1000 genomes]
rs2075215	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2075216	0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2192939	0.82[ASN][1000 genomes]
rs2216114	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2251879	0.82[ASN][1000 genomes]
rs2255991	0.84[JPT][hapmap]
rs2268988	0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2287091	0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs2287092	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2300886	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2300887	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2300888	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2300891	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2300894	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2300895	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2300896	0.86[ASN][1000 genomes]
rs2302649	0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2372887	0.85[ASN][1000 genomes]
rs28524149	0.81[ASN][1000 genomes]
rs3213746	0.85[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3755192	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs3770749	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs3770761	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3770767	0.89[ASN][1000 genomes]
rs3815555	0.83[JPT][hapmap]
rs3821144	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4629138	0.91[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4670682	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4670684	0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4670685	0.89[JPT][hapmap]
rs59559471	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73927424	0.88[ASN][1000 genomes]
rs7593932	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs9309002	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9309003	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs952711	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs952712	0.86[CHB][hapmap];1.00[JPT][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2041838	PRKD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37460000-37468600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:37460000-37471200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:37460000-37474000	Weak transcription	Colonic Mucosa	Colon
4	chr2:37460000-37495600	Weak transcription	Small Intestine	intestine
5	chr2:37460000-37501600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:37460200-37468800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:37460200-37528600	Weak transcription	Stomach Mucosa	stomach
8	chr2:37460400-37468600	Weak transcription	Brain Angular Gyrus	brain
9	chr2:37460400-37468600	Weak transcription	Brain Germinal Matrix	brain
10	chr2:37460400-37468800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:37460400-37468800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:37460400-37469000	Weak transcription	HMEC	breast
13	chr2:37460400-37470600	Weak transcription	Fetal Kidney	kidney
14	chr2:37460400-37471200	Weak transcription	Brain Hippocampus Middle	brain
15	chr2:37460400-37472200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:37460400-37472400	Weak transcription	Brain Substantia Nigra	brain
17	chr2:37460400-37476600	Weak transcription	Right Ventricle	heart
18	chr2:37460400-37481600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr2:37460400-37492200	Weak transcription	Fetal Heart	heart
20	chr2:37460400-37498600	Weak transcription	Gastric	stomach
21	chr2:37460600-37468600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr2:37460600-37468600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr2:37460600-37468800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:37460600-37471200	Weak transcription	Fetal Brain Male	brain
25	chr2:37460600-37488000	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr2:37460600-37493400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:37460600-37498600	Weak transcription	Spleen	Spleen
28	chr2:37461000-37488200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:37461000-37489800	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr2:37461200-37468800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr2:37461200-37471400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:37461200-37518800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr2:37461800-37486800	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr2:37462000-37473400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr2:37462000-37487200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr2:37462000-37488000	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:37462200-37471000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:37462200-37473200	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr2:37462400-37470800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr2:37462400-37472800	Weak transcription	NHEK	skin
41	chr2:37462400-37474000	Weak transcription	Aorta	Aorta
42	chr2:37462400-37479200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:37462600-37468600	Weak transcription	GM12878-XiMat	blood
44	chr2:37462600-37470400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:37462600-37473800	Weak transcription	Ovary	ovary
46	chr2:37462800-37468600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr2:37462800-37471000	Weak transcription	Thymus	Thymus
48	chr2:37463000-37470200	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr2:37463200-37469600	Strong transcription	Fetal Thymus	thymus
50	chr2:37463200-37470600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links