Variant report

Variant	rs7601628
Chromosome Location	chr2:37465429-37465430
allele	C/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	HDAC2	chr2:37465309-37465661	K562	blood:	n/a	n/a
2	RCOR1	chr2:37465347-37465702	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:37464697..37467448-chr2:37467935..37469545,2	K562	blood:
2	chr2:37455370..37456889-chr2:37465153..37467746,2	MCF-7	breast:
3	chr2:37464823..37466486-chr2:37471416..37473912,2	K562	blood:

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

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10177970	0.92[EUR][1000 genomes]
rs10178975	0.91[EUR][1000 genomes]
rs11124575	0.92[EUR][1000 genomes]
rs12611683	0.84[EUR][1000 genomes]
rs12712530	0.91[EUR][1000 genomes]
rs13409250	0.95[EUR][1000 genomes]
rs1861444	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2041837	0.96[EUR][1000 genomes]
rs2041840	0.96[EUR][1000 genomes]
rs2110962	0.92[EUR][1000 genomes]
rs2110964	0.96[EUR][1000 genomes]
rs2160391	0.84[EUR][1000 genomes]
rs2160392	0.91[EUR][1000 genomes]
rs2160393	0.91[EUR][1000 genomes]
rs2160395	0.96[EUR][1000 genomes]
rs2372888	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2372990	0.90[EUR][1000 genomes]
rs2430494	0.93[EUR][1000 genomes]
rs2465488	0.83[EUR][1000 genomes]
rs2540972	0.84[EUR][1000 genomes]
rs2540973	0.84[EUR][1000 genomes]
rs2540977	0.96[EUR][1000 genomes]
rs2714470	0.95[EUR][1000 genomes]
rs3902740	0.91[EUR][1000 genomes]
rs4670678	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4670687	0.84[EUR][1000 genomes]
rs4670691	0.87[EUR][1000 genomes]
rs6544065	0.92[EUR][1000 genomes]
rs6730503	0.89[EUR][1000 genomes]
rs6742641	0.89[EUR][1000 genomes]
rs7579990	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs759461	0.93[EUR][1000 genomes]
rs7602924	0.90[EUR][1000 genomes]
rs8243	0.95[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7601628	PRKD3	cis	intralobular white matter	BrainEAC
rs7601628	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	chr2:37460000-37468200	Weak transcription	Psoas Muscle	Psoas
2	chr2:37460000-37468600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:37460000-37471200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:37460000-37474000	Weak transcription	Colonic Mucosa	Colon
5	chr2:37460000-37495600	Weak transcription	Small Intestine	intestine
6	chr2:37460000-37501600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:37460200-37466600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:37460200-37468400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:37460200-37468800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:37460200-37528600	Weak transcription	Stomach Mucosa	stomach
11	chr2:37460400-37465600	Weak transcription	Left Ventricle	heart
12	chr2:37460400-37465800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:37460400-37466000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr2:37460400-37466200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:37460400-37466200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr2:37460400-37467200	Weak transcription	Esophagus	oesophagus
17	chr2:37460400-37467200	Weak transcription	Pancreas	Pancrea
18	chr2:37460400-37467400	Weak transcription	NHDF-Ad	bronchial
19	chr2:37460400-37468000	Weak transcription	HUVEC	blood vessel
20	chr2:37460400-37468400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr2:37460400-37468400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr2:37460400-37468400	Weak transcription	NH-A	brain
23	chr2:37460400-37468600	Weak transcription	Brain Angular Gyrus	brain
24	chr2:37460400-37468600	Weak transcription	Brain Germinal Matrix	brain
25	chr2:37460400-37468800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr2:37460400-37468800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr2:37460400-37469000	Weak transcription	HMEC	breast
28	chr2:37460400-37470600	Weak transcription	Fetal Kidney	kidney
29	chr2:37460400-37471200	Weak transcription	Brain Hippocampus Middle	brain
30	chr2:37460400-37472200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:37460400-37472400	Weak transcription	Brain Substantia Nigra	brain
32	chr2:37460400-37476600	Weak transcription	Right Ventricle	heart
33	chr2:37460400-37481600	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr2:37460400-37492200	Weak transcription	Fetal Heart	heart
35	chr2:37460400-37498600	Weak transcription	Gastric	stomach
36	chr2:37460600-37467800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr2:37460600-37468600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr2:37460600-37468600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr2:37460600-37468800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr2:37460600-37471200	Weak transcription	Fetal Brain Male	brain
41	chr2:37460600-37488000	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr2:37460600-37493400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:37460600-37498600	Weak transcription	Spleen	Spleen
44	chr2:37461000-37488200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:37461000-37489800	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr2:37461200-37467600	Strong transcription	Fetal Intestine Small	intestine
47	chr2:37461200-37467800	Strong transcription	Fetal Stomach	stomach
48	chr2:37461200-37468800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr2:37461200-37471400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:37461200-37518800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links