Variant report

Variant	rs392410
Chromosome Location	chr1:45356638-45356639
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45285269..45287517-chr1:45356537..45358662,2	K562	blood:
2	chr1:45348967..45351344-chr1:45356459..45358965,2	K562	blood:
3	chr1:45185573..45188435-chr1:45355678..45358866,3	K562	blood:

Variant related genes	Relation type
ENSG00000202444	Chromatin interaction
ENSG00000199377	Chromatin interaction

Extended variants
information (count: 153 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:149)

rs_ID	r²[population]
rs10157761	0.91[EUR][1000 genomes]
rs10159318	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10218751	0.90[EUR][1000 genomes]
rs1022814	1.00[CEU][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1114390	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11211042	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs11211043	0.93[EUR][1000 genomes]
rs11211052	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11211061	0.88[EUR][1000 genomes]
rs11211062	1.00[CEU][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes]
rs11211063	1.00[CEU][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs114833	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12057238	1.00[JPT][hapmap]
rs12080887	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12093313	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12095412	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs12402452	1.00[CEU][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs12402781	1.00[JPT][hapmap]
rs12403201	1.00[CEU][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs12404127	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12404168	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12405110	0.89[EUR][1000 genomes]
rs12405721	1.00[CEU][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12407290	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs12407565	1.00[CEU][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12408763	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12410088	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12411070	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13374816	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1392035	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1572379	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1627320	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16832249	0.89[EUR][1000 genomes]
rs16832251	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs16832301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17390300	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17390328	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17390356	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17390398	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17390824	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17390859	0.91[EUR][1000 genomes]
rs17390900	0.91[EUR][1000 genomes]
rs17390983	0.91[EUR][1000 genomes]
rs17392632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs174636	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2078329	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2102035	1.00[CEU][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2133501	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2261859	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2295996	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs263960	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs263961	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs263967	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs263971	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs263979	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs263981	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs264002	1.00[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs264004	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs264006	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs264007	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs264010	0.89[EUR][1000 genomes]
rs264015	0.89[EUR][1000 genomes]
rs28700974	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28707013	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28819230	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35700678	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs371098	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3738248	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3767490	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3795715	0.81[JPT][hapmap]
rs3795718	0.94[CEU][hapmap]
rs3889352	1.00[CEU][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3889822	1.00[CEU][hapmap];0.91[JPT][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3923304	0.93[CEU][hapmap]
rs4073112	0.93[CEU][hapmap]
rs4082644	1.00[CEU][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41269085	0.90[EUR][1000 genomes]
rs423959	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs427392	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs435311	1.00[CEU][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4415616	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs441876	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4424549	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4472791	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4515833	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs471564	1.00[CEU][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs539409	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs546354	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55708712	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55756712	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55792507	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55807836	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55851444	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55893665	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55916129	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55926235	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56102504	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57104118	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57769237	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58191426	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59050077	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59552012	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59559455	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59938994	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60082006	0.91[EUR][1000 genomes]
rs606873	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60741033	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60787198	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs608649	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61149327	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61673889	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs637224	1.00[CEU][hapmap];0.91[JPT][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs640743	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6657078	0.88[EUR][1000 genomes]
rs6684417	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67058449	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72674049	0.89[EUR][1000 genomes]
rs72674051	0.89[EUR][1000 genomes]
rs72674064	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72674081	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72674084	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72676504	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72676505	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72676509	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72676513	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72676525	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72676529	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72676536	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72676539	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72676542	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72676550	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72676553	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72676555	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72676557	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72676559	0.97[EUR][1000 genomes]
rs72676561	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72676563	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72676581	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72676600	0.88[EUR][1000 genomes]
rs72677810	0.91[EUR][1000 genomes]
rs7515226	1.00[CEU][hapmap];0.89[JPT][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7519592	1.00[CEU][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7529213	1.00[CEU][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7529221	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7531391	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7533716	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7546853	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9662872	0.88[EUR][1000 genomes]
rs9662878	0.88[EUR][1000 genomes]

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	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
2	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
3	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
4	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45309200-45360600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr1:45313400-45360200	Weak transcription	Hela-S3	cervix
3	chr1:45322600-45360000	Weak transcription	Small Intestine	intestine
4	chr1:45332600-45357200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:45333400-45357000	Weak transcription	Fetal Kidney	kidney
6	chr1:45334600-45371800	Weak transcription	Gastric	stomach
7	chr1:45340800-45361800	Weak transcription	Aorta	Aorta
8	chr1:45345600-45366200	Weak transcription	Esophagus	oesophagus
9	chr1:45345800-45363600	Weak transcription	Colonic Mucosa	Colon
10	chr1:45346200-45359200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:45346400-45363200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr1:45347600-45358800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:45347600-45360400	Weak transcription	HMEC	breast
14	chr1:45347600-45362600	Weak transcription	Lung	lung
15	chr1:45347600-45410800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:45348000-45360000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:45349000-45357000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:45349600-45358400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:45349600-45360000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr1:45350600-45360600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:45350600-45361200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:45350800-45363200	Weak transcription	Right Ventricle	heart
23	chr1:45350800-45363400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:45350800-45364200	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:45350800-45369000	Weak transcription	Brain Angular Gyrus	brain
26	chr1:45350800-45382400	Weak transcription	Pancreas	Pancrea
27	chr1:45350800-45411800	Weak transcription	Left Ventricle	heart
28	chr1:45351400-45357800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
29	chr1:45351400-45358200	ZNF genes & repeats	Fetal Intestine Small	intestine
30	chr1:45351800-45357200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
31	chr1:45351800-45357200	ZNF genes & repeats	Fetal Muscle Leg	muscle
32	chr1:45351800-45358600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:45352000-45358200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
34	chr1:45352200-45357800	ZNF genes & repeats	Dnd41	blood
35	chr1:45352200-45358200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:45352400-45358200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
37	chr1:45352600-45357600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:45352600-45360400	Weak transcription	Ovary	ovary
39	chr1:45353000-45357200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:45353000-45357800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:45353000-45374000	Weak transcription	Fetal Heart	heart
42	chr1:45354000-45357200	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
43	chr1:45354200-45357600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
44	chr1:45354400-45356800	ZNF genes & repeats	HSMMtube	muscle
45	chr1:45354400-45357400	ZNF genes & repeats	Fetal Brain Female	brain
46	chr1:45354400-45357400	ZNF genes & repeats	NH-A	brain
47	chr1:45354800-45358400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:45354800-45359600	Weak transcription	Osteobl	bone
49	chr1:45354800-45360000	Weak transcription	NHEK	skin
50	chr1:45355000-45357000	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links