Variant report

Variant	rs10022673
Chromosome Location	chr4:76458378-76458379
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10009558	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10018377	0.86[EUR][1000 genomes]
rs10020976	0.87[EUR][1000 genomes]
rs10026125	0.85[EUR][1000 genomes]
rs10518139	0.86[EUR][1000 genomes]
rs13103482	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13134862	0.90[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs13137105	0.87[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs28504656	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28609645	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28871288	0.86[EUR][1000 genomes]
rs28877578	0.90[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs34402235	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35362134	0.87[EUR][1000 genomes]
rs35931543	0.87[EUR][1000 genomes]
rs62318629	0.86[EUR][1000 genomes]
rs62318632	0.87[EUR][1000 genomes]
rs6835573	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6838603	0.86[EUR][1000 genomes]
rs7657576	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7661260	0.86[ASN][1000 genomes]
rs7685936	0.87[EUR][1000 genomes]
rs7699102	0.87[EUR][1000 genomes]
rs9307834	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv594687	chr4:76154064-76502748	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv534570	chr4:76214619-76498362	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10022673	RCHY1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76440400-76458800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:76440400-76466400	Weak transcription	Small Intestine	intestine
3	chr4:76440400-76473200	Weak transcription	Gastric	stomach
4	chr4:76440800-76458600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:76441600-76458600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr4:76441600-76459200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:76443200-76458800	Weak transcription	Stomach Mucosa	stomach
8	chr4:76443400-76470200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr4:76444400-76461000	Weak transcription	A549	lung
10	chr4:76444400-76471800	Weak transcription	Fetal Brain Male	brain
11	chr4:76445800-76458600	Strong transcription	Liver	Liver
12	chr4:76446200-76458400	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr4:76446200-76458400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr4:76450200-76458400	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr4:76450400-76458400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:76450800-76458800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:76451600-76474400	Weak transcription	Psoas Muscle	Psoas
18	chr4:76452600-76468000	Weak transcription	NHLF	lung
19	chr4:76452600-76477400	Weak transcription	Colon Smooth Muscle	Colon
20	chr4:76453200-76473600	Weak transcription	Brain Angular Gyrus	brain
21	chr4:76454200-76458800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr4:76454600-76458800	Strong transcription	Primary T cells from cord blood	blood
23	chr4:76454600-76459000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr4:76454600-76459000	Strong transcription	Fetal Lung	lung
25	chr4:76454800-76459200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr4:76455000-76469400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr4:76455000-76470200	Weak transcription	Brain Substantia Nigra	brain
28	chr4:76455000-76470800	Weak transcription	NHDF-Ad	bronchial
29	chr4:76455200-76458800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr4:76455400-76458400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr4:76455400-76458800	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr4:76455400-76459000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr4:76456000-76459000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr4:76456000-76459000	ZNF genes & repeats	Fetal Intestine Small	intestine
35	chr4:76456000-76473000	Weak transcription	HepG2	liver
36	chr4:76456200-76458600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
37	chr4:76456200-76459200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
38	chr4:76456200-76460400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr4:76456400-76459000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
40	chr4:76456400-76471600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr4:76456600-76459000	ZNF genes & repeats	Brain Germinal Matrix	brain
42	chr4:76456600-76461600	Weak transcription	NH-A	brain
43	chr4:76456600-76467400	Weak transcription	HMEC	breast
44	chr4:76456600-76467400	Weak transcription	Osteobl	bone
45	chr4:76456600-76471000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr4:76456600-76473200	Weak transcription	Fetal Heart	heart
47	chr4:76456800-76458400	Weak transcription	K562	blood
48	chr4:76456800-76458600	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr4:76456800-76458600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr4:76456800-76459000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood

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