Variant report

Variant	rs2185971
Chromosome Location	chr1:114220305-114220306
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114212058..114214688-chr1:114217824..114221724,4	K562	blood:
2	chr1:114210224..114212923-chr1:114219476..114221721,2	MCF-7	breast:
3	chr1:114212026..114215527-chr1:114217715..114221049,6	K562	blood:
4	chr1:113682753..113683817-chr1:114220119..114221170,5	MCF-7	breast:
5	chr1:113931113..113934669-chr1:114216801..114220484,4	MCF-7	breast:
6	chr1:113932659..113933643-chr1:114220188..114220916,2	MCF-7	breast:
7	chr1:113681992..113683537-chr1:114220198..114221993,2	MCF-7	breast:
8	chr1:114217666..114220401-chr3:64471465..64473065,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000081026	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10858016	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11102671	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1111695	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1113523	0.84[LWK][hapmap];0.94[YRI][hapmap]
rs12061482	0.81[ASW][hapmap]
rs1217204	0.94[YRI][hapmap]
rs1217211	0.81[YRI][hapmap]
rs1217226	0.81[ASW][hapmap];0.84[LWK][hapmap];0.94[YRI][hapmap]
rs1217227	0.81[ASW][hapmap];0.83[LWK][hapmap];0.94[YRI][hapmap]
rs1217228	0.81[ASW][hapmap];0.83[LWK][hapmap];0.94[YRI][hapmap]
rs1217236	0.81[ASW][hapmap];0.80[LWK][hapmap];0.88[YRI][hapmap]
rs1217379	0.82[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs1217385	0.90[CHD][hapmap];0.95[GIH][hapmap]
rs1217406	0.82[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.81[TSI][hapmap]
rs1217418	0.81[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs1217419	0.82[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs1230682	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1230686	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1235005	0.95[CHD][hapmap];0.97[GIH][hapmap]
rs1777238	0.81[AFR][1000 genomes]
rs1777241	0.81[ASW][hapmap]
rs1936398	0.81[ASW][hapmap]
rs1981319	0.81[ASW][hapmap]
rs2146019	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2273758	0.83[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2295853	0.81[ASW][hapmap]
rs2476600	0.81[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.83[TSI][hapmap]
rs2797414	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2797416	0.82[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs3789598	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs3789600	0.82[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs4600045	0.81[ASW][hapmap]
rs4839335	0.89[AFR][1000 genomes]
rs6537798	0.82[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs6665194	0.90[CHD][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap]
rs6672018	0.83[ASW][hapmap];0.82[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs6696784	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6698586	0.81[ASW][hapmap]
rs7555634	0.82[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs7556622	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872161	chr1:114162194-114280135	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2185971	PHTF1	cis	parietal	SCAN
rs2185971	PHTF1	cis	cerebellum	SCAN
rs2185971	SIKE1	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114171600-114241400	Weak transcription	Right Ventricle	heart
2	chr1:114173000-114226800	Weak transcription	Aorta	Aorta
3	chr1:114173800-114236000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:114179800-114239600	Weak transcription	Spleen	Spleen
5	chr1:114183000-114235800	Weak transcription	Dnd41	blood
6	chr1:114185200-114224400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:114185400-114228000	Weak transcription	HepG2	liver
8	chr1:114185800-114223600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:114194000-114223600	Weak transcription	Left Ventricle	heart
10	chr1:114196600-114226400	Weak transcription	Gastric	stomach
11	chr1:114200200-114227800	Weak transcription	Stomach Mucosa	stomach
12	chr1:114202000-114241400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:114203000-114232000	Weak transcription	Fetal Brain Female	brain
14	chr1:114203000-114237800	Weak transcription	NH-A	brain
15	chr1:114203200-114224800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:114203200-114232200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:114203200-114237600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:114203200-114298600	Weak transcription	Fetal Brain Male	brain
19	chr1:114203400-114237800	Weak transcription	Brain Angular Gyrus	brain
20	chr1:114206600-114223600	Weak transcription	Hela-S3	cervix
21	chr1:114206600-114226400	Weak transcription	NHLF	lung
22	chr1:114206600-114229800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:114207400-114230600	Weak transcription	NHEK	skin
24	chr1:114209600-114229600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:114209800-114232400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr1:114211200-114231400	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr1:114211600-114234600	Weak transcription	Brain Germinal Matrix	brain
28	chr1:114213000-114221800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:114213400-114225400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:114213600-114232000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:114213600-114241600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:114214800-114232400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:114215000-114226800	Weak transcription	Ovary	ovary
34	chr1:114215400-114235800	Weak transcription	Esophagus	oesophagus
35	chr1:114215400-114235800	Weak transcription	Lung	lung
36	chr1:114216000-114247000	Weak transcription	HMEC	breast
37	chr1:114216200-114225800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr1:114216200-114241600	Weak transcription	Pancreas	Pancrea
39	chr1:114216200-114279800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr1:114216400-114223600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:114216400-114223600	Weak transcription	Fetal Muscle Leg	muscle
42	chr1:114216400-114232000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:114216400-114250400	Weak transcription	Placenta	Placenta
44	chr1:114216600-114220400	Weak transcription	Colon Smooth Muscle	Colon
45	chr1:114216600-114225600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:114216600-114225600	Weak transcription	Duodenum Mucosa	Duodenum
47	chr1:114216600-114227600	Weak transcription	Fetal Thymus	thymus
48	chr1:114216800-114222800	Weak transcription	Fetal Intestine Small	intestine
49	chr1:114216800-114226400	Weak transcription	Primary T cells from cord blood	blood
50	chr1:114217200-114224800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links