Variant report

Variant	rs6852388
Chromosome Location	chr4:107011960-107011961
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10000428	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10003024	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10004611	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10008428	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10008773	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10016884	0.99[ASN][1000 genomes]
rs10017969	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10018910	1.00[ASN][1000 genomes]
rs10025052	0.82[EUR][1000 genomes]
rs10027207	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10030019	0.83[EUR][1000 genomes]
rs10049933	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11097912	0.83[EUR][1000 genomes]
rs11732251	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11732791	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11931386	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11932523	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11942153	0.82[EUR][1000 genomes]
rs12509366	0.84[EUR][1000 genomes]
rs12509640	0.82[EUR][1000 genomes]
rs12510966	0.82[EUR][1000 genomes]
rs12512683	0.83[EUR][1000 genomes]
rs12513345	0.88[ASN][1000 genomes]
rs12642691	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12642900	0.82[EUR][1000 genomes]
rs12650692	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13101612	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13113845	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13114479	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13121614	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13138528	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17272618	1.00[ASN][1000 genomes]
rs28391259	0.82[EUR][1000 genomes]
rs28394440	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28467469	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28784652	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28805707	0.99[ASN][1000 genomes]
rs28822186	0.84[EUR][1000 genomes]
rs28845843	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28897193	0.81[EUR][1000 genomes]
rs3109955	0.94[ASN][1000 genomes]
rs3109958	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3109960	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3113249	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3113250	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3113252	0.94[ASN][1000 genomes]
rs3133168	0.94[ASN][1000 genomes]
rs4306956	0.92[EUR][1000 genomes]
rs4307042	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4314353	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4355394	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4364267	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4374692	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4382109	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4470632	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4508971	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4569824	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4577583	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4600995	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55633564	0.82[EUR][1000 genomes]
rs60538413	0.96[EUR][1000 genomes]
rs62321365	0.82[EUR][1000 genomes]
rs6533237	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6533242	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6819081	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6823347	0.81[EUR][1000 genomes]
rs6824682	0.83[EUR][1000 genomes]
rs6828362	0.84[EUR][1000 genomes]
rs6836198	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6842919	0.95[EUR][1000 genomes]
rs6843331	0.94[EUR][1000 genomes]
rs6844105	1.00[ASN][1000 genomes]
rs6846579	0.82[EUR][1000 genomes]
rs6849573	1.00[ASN][1000 genomes]
rs6853554	0.88[ASN][1000 genomes]
rs72677306	0.84[EUR][1000 genomes]
rs7356287	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7438546	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7657962	0.82[EUR][1000 genomes]
rs7662592	0.84[EUR][1000 genomes]
rs7667596	0.95[ASN][1000 genomes]
rs7668276	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7673101	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7677248	0.82[EUR][1000 genomes]
rs7678847	0.83[EUR][1000 genomes]
rs7682646	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7687657	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7689298	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7692069	0.82[EUR][1000 genomes]
rs7692652	0.91[ASN][1000 genomes]
rs7693333	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7693448	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9685464	0.84[EUR][1000 genomes]
rs9991091	0.83[EUR][1000 genomes]
rs9996093	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3414280	chr4:106987397-107017178	ZNF genes & repeats Weak transcription Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
2	esv3419151	chr4:106987397-107020894	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
3	esv1799793	chr4:107000462-107062671	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv1801716	chr4:107000462-107062671	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv1849248	chr4:107000462-107062671	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv1850577	chr4:107000462-107062671	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6852388	SCYE1	Cis_1M	lymphoblastoid	RTeQTL
rs6852388	MGC16169	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106994600-107015000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr4:106997200-107031000	Weak transcription	Psoas Muscle	Psoas
3	chr4:106999000-107012000	Weak transcription	NHDF-Ad	bronchial
4	chr4:107001200-107018600	Weak transcription	HUVEC	blood vessel
5	chr4:107008800-107013000	ZNF genes & repeats	Adipose Nuclei	Adipose
6	chr4:107008800-107013600	Weak transcription	NHLF	lung
7	chr4:107009000-107012200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr4:107009000-107012800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
9	chr4:107009400-107012600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:107009600-107012000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr4:107009600-107012600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:107009600-107012800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
13	chr4:107009600-107014800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
14	chr4:107009800-107012600	ZNF genes & repeats	Fetal Brain Female	brain
15	chr4:107009800-107012600	Strong transcription	Fetal Kidney	kidney
16	chr4:107009800-107012800	ZNF genes & repeats	Aorta	Aorta
17	chr4:107009800-107012800	ZNF genes & repeats	Liver	Liver
18	chr4:107009800-107013000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
19	chr4:107009800-107014200	ZNF genes & repeats	Lung	lung
20	chr4:107010000-107012600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:107010000-107012600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:107010000-107012800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:107010000-107012800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
24	chr4:107010000-107012800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
25	chr4:107010000-107012800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
26	chr4:107010000-107012800	ZNF genes & repeats	Fetal Muscle Leg	muscle
27	chr4:107010000-107012800	ZNF genes & repeats	Left Ventricle	heart
28	chr4:107010000-107012800	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
29	chr4:107010000-107014200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr4:107010000-107014200	ZNF genes & repeats	Esophagus	oesophagus
31	chr4:107010000-107014400	ZNF genes & repeats	Fetal Intestine Small	intestine
32	chr4:107010000-107014600	ZNF genes & repeats	Fetal Stomach	stomach
33	chr4:107010200-107012400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
34	chr4:107010200-107012600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr4:107010200-107012600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:107010200-107012800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
37	chr4:107010200-107012800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:107010200-107012800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
39	chr4:107010200-107012800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr4:107010200-107014200	ZNF genes & repeats	Placenta	Placenta
41	chr4:107010200-107025400	Weak transcription	Small Intestine	intestine
42	chr4:107010400-107012200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
43	chr4:107010400-107012600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
44	chr4:107010400-107012600	ZNF genes & repeats	HSMM	muscle
45	chr4:107010400-107012800	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
46	chr4:107010400-107012800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
47	chr4:107010400-107013000	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
48	chr4:107010600-107012400	ZNF genes & repeats	Brain Angular Gyrus	brain
49	chr4:107010600-107012800	ZNF genes & repeats	Primary B cells from cord blood	blood
50	chr4:107010600-107012800	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links