Variant report

Variant	rs2417984
Chromosome Location	chr12:21601932-21601933
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10161130	0.88[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs10161132	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs10437776	0.91[CHB][hapmap]
rs10770808	0.91[CHB][hapmap]
rs10770810	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10841808	0.92[CHB][hapmap]
rs10841809	0.92[CHB][hapmap]
rs10841810	0.95[CHB][hapmap]
rs10841815	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs10841832	0.81[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap]
rs11046050	0.96[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs11046055	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11046064	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs11046065	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs11608682	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs11610942	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12318289	0.83[CHB][hapmap]
rs12372774	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs13035	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1476904	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs1476905	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1476907	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs1860949	0.96[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs1963817	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2058463	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2058464	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs2110165	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs2159943	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs2159948	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2192183	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs2215734	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2284392	0.86[CHB][hapmap]
rs2302500	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs2417979	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2417980	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs2417981	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs2417982	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs3752648	0.84[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap]
rs3759229	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3782660	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs3825287	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4762829	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs4762830	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs4762831	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs6487222	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6487223	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6487224	0.84[CEU][hapmap]
rs6487228	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs6487229	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6487230	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs6487231	0.96[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs6487233	0.81[CHB][hapmap]
rs7134243	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs7135390	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7136175	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs7136257	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs7136265	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs7137034	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs714356	0.96[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs714357	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs7295570	0.96[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs7298300	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs7303408	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs7310953	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7314170	0.82[CHB][hapmap]
rs738028	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs7970416	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7974260	0.91[CEU][hapmap]
rs917855	0.81[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]
rs997820	0.91[CHB][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898895	chr12:21561645-21621891	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
2	nsv898896	chr12:21561645-21695584	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2417984	LOC642732///PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs2417984	PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs2417984	RECQL	Cis_1M	lymphoblastoid	RTeQTL
rs2417984	LOC642732	Cis_1M	lymphoblastoid	RTeQTL
rs2417984	FLJ22028	cis	normal skin	skin_eQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21591400-21602800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:21591600-21609000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:21591600-21609000	Weak transcription	Brain Angular Gyrus	brain
4	chr12:21591600-21609200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr12:21591800-21609000	Weak transcription	Fetal Heart	heart
6	chr12:21591800-21611000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr12:21591800-21614600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr12:21591800-21614800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr12:21591800-21621000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:21591800-21624200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr12:21592000-21614200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr12:21592000-21620600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:21592000-21631000	Weak transcription	Psoas Muscle	Psoas
14	chr12:21592200-21609000	Weak transcription	NH-A	brain
15	chr12:21592200-21609000	Weak transcription	NHDF-Ad	bronchial
16	chr12:21592200-21609200	Weak transcription	Brain Substantia Nigra	brain
17	chr12:21592400-21610400	Weak transcription	NHEK	skin
18	chr12:21592600-21609200	Weak transcription	Small Intestine	intestine
19	chr12:21592800-21631400	Weak transcription	K562	blood
20	chr12:21593400-21604400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:21593400-21606600	Strong transcription	Liver	Liver
22	chr12:21593400-21609000	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr12:21593400-21609000	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr12:21593400-21617800	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr12:21594000-21617600	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr12:21594800-21605800	Strong transcription	Fetal Thymus	thymus
27	chr12:21594800-21613200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:21595200-21608800	Weak transcription	HMEC	breast
29	chr12:21595600-21602200	Weak transcription	Osteobl	bone
30	chr12:21595600-21609200	Weak transcription	Colonic Mucosa	Colon
31	chr12:21595600-21626200	Weak transcription	Right Ventricle	heart
32	chr12:21595800-21606400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr12:21595800-21609000	Weak transcription	Brain Germinal Matrix	brain
34	chr12:21595800-21609000	Weak transcription	HSMMtube	muscle
35	chr12:21595800-21609200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr12:21595800-21609200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr12:21595800-21610400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr12:21595800-21611000	Weak transcription	HepG2	liver
39	chr12:21595800-21624400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr12:21595800-21631400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr12:21595800-21632600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr12:21595800-21633200	Weak transcription	Gastric	stomach
43	chr12:21595800-21650000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr12:21596000-21605000	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr12:21596000-21611800	Weak transcription	Aorta	Aorta
46	chr12:21596000-21631600	Weak transcription	Pancreas	Pancrea
47	chr12:21596200-21625000	Weak transcription	NHLF	lung
48	chr12:21596400-21603400	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr12:21596800-21602200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr12:21596800-21604600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links