Variant report

Variant	rs2993531
Chromosome Location	chr1:212190116-212190117
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212189353..212195242-chr1:212205107..212211524,11	K562	blood:
2	chr1:212190110..212192373-chr1:212222037..212223610,2	K562	blood:
3	chr1:212188937..212191078-chr1:212212005..212214443,2	MCF-7	breast:
4	chr1:212189325..212191475-chr1:212197899..212201793,4	K562	blood:
5	chr1:212183318..212187714-chr1:212189171..212192527,3	K562	blood:

Variant related genes	Relation type
ENSG00000143476	Chromatin interaction
ENSG00000212187	Chromatin interaction
ENSG00000143493	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1316820	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1578992	0.86[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1578993	0.89[ASW][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap]
rs1933593	0.94[ASW][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.84[MKK][hapmap];0.86[YRI][hapmap]
rs2130503	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2358386	0.94[ASW][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap]
rs2358440	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2788139	0.81[JPT][hapmap]
rs2788140	0.89[ASW][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap]
rs2808392	0.90[JPT][hapmap];0.86[YRI][hapmap]
rs2884428	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2970592	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2970599	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2970601	0.90[JPT][hapmap];0.83[YRI][hapmap]
rs2993528	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2993529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2993533	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2993534	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2993544	0.90[JPT][hapmap];0.82[YRI][hapmap]
rs3009985	0.81[ASN][1000 genomes]
rs3010003	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3010004	0.82[JPT][hapmap]
rs3010006	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3010023	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3010024	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3738449	0.94[ASW][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];0.84[MKK][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap]
rs4951435	0.88[ASN][1000 genomes]
rs6657728	0.86[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs6684814	0.82[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2993531	PROX1	cis	cerebellum	SCAN
rs2993531	C1orf74	cis	cerebellum	SCAN
rs2993531	INTS7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212112800-212202000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr1:212123800-212198200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:212129400-212204000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:212133800-212208000	Weak transcription	Gastric	stomach
5	chr1:212134000-212207600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr1:212134000-212207800	Weak transcription	Colonic Mucosa	Colon
7	chr1:212136600-212204000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:212148800-212207600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:212149200-212199800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:212152800-212201600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:212153400-212203600	Weak transcription	Psoas Muscle	Psoas
12	chr1:212153600-212202600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:212160200-212199800	Weak transcription	Brain Substantia Nigra	brain
14	chr1:212160200-212202600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr1:212170200-212191400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:212170200-212197600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:212170400-212202600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:212170600-212194200	Weak transcription	Placenta	Placenta
19	chr1:212170800-212199200	Weak transcription	Pancreas	Pancrea
20	chr1:212170800-212207800	Weak transcription	Right Ventricle	heart
21	chr1:212171000-212199800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:212171200-212197800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:212171200-212208000	Weak transcription	Esophagus	oesophagus
24	chr1:212171200-212208000	Weak transcription	Lung	lung
25	chr1:212171400-212197800	Weak transcription	Aorta	Aorta
26	chr1:212171600-212198000	Weak transcription	Fetal Kidney	kidney
27	chr1:212171600-212198200	Weak transcription	Small Intestine	intestine
28	chr1:212171600-212207400	Weak transcription	Fetal Stomach	stomach
29	chr1:212171800-212191400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:212171800-212197600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr1:212171800-212207600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:212172200-212199800	Weak transcription	Stomach Mucosa	stomach
33	chr1:212173000-212204200	Weak transcription	Fetal Heart	heart
34	chr1:212180400-212206800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:212180600-212190600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:212180800-212204000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:212181000-212193000	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr1:212181000-212197800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:212181600-212193800	Weak transcription	Ovary	ovary
40	chr1:212181600-212198000	Weak transcription	NHLF	lung
41	chr1:212182000-212193600	Weak transcription	HSMMtube	muscle
42	chr1:212182000-212193800	Weak transcription	Left Ventricle	heart
43	chr1:212182200-212205000	Weak transcription	Thymus	Thymus
44	chr1:212183200-212197800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr1:212183200-212200400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:212183200-212202600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:212183400-212197800	Weak transcription	HUVEC	blood vessel
48	chr1:212183600-212199800	Weak transcription	Brain Hippocampus Middle	brain
49	chr1:212184000-212198000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr1:212184200-212193200	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links