Variant report

Variant	rs62318629
Chromosome Location	chr4:76422717-76422718
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PBX3	chr4:76422287-76422774	SK-N-SH	brain:	n/a	n/a
2	FOXM1	chr4:76422439-76422721	MCF-7	breast:	n/a	n/a
3	PBX3	chr4:76422339-76422801	SK-N-SH	brain:	n/a	n/a
4	STAT3	chr4:76422332-76422740	MCF10A-Er-Src	breast:	n/a	n/a
5	FOXM1	chr4:76422257-76422911	SK-N-SH	brain:	n/a	n/a
6	E2F4	chr4:76422518-76422738	MCF10A-Er-Src	breast:	n/a	n/a
7	MYC	chr4:76422333-76422853	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:76415601..76419005-chr4:76420514..76424216,3	K562	blood:
2	chr4:76421225..76424170-chr4:76432854..76436484,3	K562	blood:
3	chr4:76420497..76422947-chr4:76425693..76428176,3	K562	blood:

Variant related genes	Relation type
RCHY1	TF binding region
ENSG00000163743	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10009558	0.86[EUR][1000 genomes]
rs10018377	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10020976	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10022673	0.86[EUR][1000 genomes]
rs10026125	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10518139	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13103482	0.86[EUR][1000 genomes]
rs13134862	0.87[EUR][1000 genomes]
rs13137105	0.87[EUR][1000 genomes]
rs1841933	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs28609645	0.85[EUR][1000 genomes]
rs28871288	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28877578	0.87[EUR][1000 genomes]
rs34402235	0.86[EUR][1000 genomes]
rs35362134	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35931543	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62318632	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835573	0.86[EUR][1000 genomes]
rs6838603	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7657576	0.86[EUR][1000 genomes]
rs7681108	0.88[ASN][1000 genomes]
rs7685936	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7699102	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307834	0.86[EUR][1000 genomes]
rs9998576	0.85[AMR][1000 genomes];0.80[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
rs62318629	RCHY1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76392600-76434800	Weak transcription	Gastric	stomach
2	chr4:76394600-76424600	Weak transcription	Right Ventricle	heart
3	chr4:76395800-76437000	Weak transcription	Aorta	Aorta
4	chr4:76395800-76437000	Weak transcription	Lung	lung
5	chr4:76395800-76437000	Weak transcription	Pancreas	Pancrea
6	chr4:76396200-76424400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:76396200-76437000	Weak transcription	Esophagus	oesophagus
8	chr4:76397800-76437000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:76398200-76434200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr4:76398800-76437200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:76399400-76434400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr4:76400600-76437000	Weak transcription	Spleen	Spleen
13	chr4:76401000-76436200	Weak transcription	Brain Angular Gyrus	brain
14	chr4:76402200-76423000	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr4:76402200-76425800	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr4:76402400-76425800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:76402600-76423200	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr4:76403000-76423800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr4:76403800-76433600	Strong transcription	Primary B cells from peripheral blood	blood
20	chr4:76404400-76422800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:76404800-76422800	Strong transcription	Dnd41	blood
22	chr4:76405600-76434400	Weak transcription	Fetal Heart	heart
23	chr4:76406000-76436600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr4:76406600-76438800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr4:76407800-76424600	Weak transcription	Fetal Brain Male	brain
26	chr4:76408000-76424600	Weak transcription	Ovary	ovary
27	chr4:76408000-76436600	Weak transcription	Hela-S3	cervix
28	chr4:76409400-76425800	Strong transcription	Fetal Thymus	thymus
29	chr4:76409600-76423800	Weak transcription	Fetal Brain Female	brain
30	chr4:76410000-76437200	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr4:76410400-76425600	Strong transcription	Duodenum Mucosa	Duodenum
32	chr4:76411400-76435400	Weak transcription	Small Intestine	intestine
33	chr4:76412200-76425000	Weak transcription	Fetal Intestine Small	intestine
34	chr4:76413400-76423000	Strong transcription	Primary B cells from cord blood	blood
35	chr4:76414600-76427000	Weak transcription	Fetal Stomach	stomach
36	chr4:76414600-76429400	Weak transcription	HSMMtube	muscle
37	chr4:76415000-76424600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr4:76415200-76423400	Weak transcription	Psoas Muscle	Psoas
39	chr4:76415200-76428200	Weak transcription	A549	lung
40	chr4:76415400-76424000	Weak transcription	Brain Hippocampus Middle	brain
41	chr4:76415400-76430200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr4:76415400-76435600	Weak transcription	Brain Substantia Nigra	brain
43	chr4:76415400-76436400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr4:76415800-76430200	Weak transcription	Colonic Mucosa	Colon
45	chr4:76416000-76423800	Weak transcription	Fetal Kidney	kidney
46	chr4:76416000-76424400	Weak transcription	Fetal Muscle Trunk	muscle
47	chr4:76416000-76429400	Weak transcription	Left Ventricle	heart
48	chr4:76416200-76424400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr4:76416600-76426600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr4:76416600-76436200	Weak transcription	Brain Anterior Caudate	brain

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